Package 'iSEE'

Add custom label plotting commands

Description

Add ggplot instructions to add custom labels to specified points in a DotPlot. This is a utility function that is intended for use in .generateDotPlot.

Usage

.addCustomLabelsCommands(x, commands, plot_type)

Arguments

x	An instance of a DotPlot class.
commands	A character vector representing the sequence of commands to create the ggplot object.
plot_type	String specifying the type of plot, e.g., "scatter", "square", "violin".

Value

A character vector containing commands plus any additional commands required to generate the labels.

Author(s)

Kevin Rue-Albrecht, Aaron Lun

---

Add centered label plotting commands

Description

Add ggplot instructions to label the center of each group on a scatter plot. This is a utility function that is intended for use in .generateDotPlot.

Usage

.addLabelCentersCommands(x, commands)

Arguments

x	An instance of a DotPlot class.
commands	A character vector representing the sequence of commands to create the ggplot object.

Value

A character vector containing commands plus any additional commands required to generate the labels.

Author(s)

Aaron Lun

---

Add multiple selection plotting commands

Description

Add ggplot instructions to create brushes and lassos for both saved and active multiple selections in a DotPlot panel.

Usage

.addMultiSelectionPlotCommands(x, envir, commands, flip = FALSE)

Arguments

x	An instance of a DotPlot class.
envir	The environment in which the ggplot commands are to be evaluated.
commands	A character vector representing the sequence of commands to create the ggplot object.
flip	A logical scalar indicating whether the x- and y-axes are flipped, only relevant to horizontal violin plots.

Details

This is a utility function that is intended for use in .generateDotPlot. It will modify envir by adding all_active and all_saved variables, so developers should not use these names for their own variables in envir.

If no self-selection structures exist in x, commands is returned directly without modification.

Value

A character vector containing commands plus any additional commands required to draw the self selections.

Author(s)

Aaron Lun

---

Add a step to the tour

Description

Utility to add a step to the panel-specific rintrojs tour, generating the element tag automatically.

Usage

.addTourStep(x, field, text, is_selectize = FALSE)

Arguments

x	A Panel object to be toured.
field	String containing the name of the slot of x, itself corresponding to an interface element to highlight.
text	String containing the text to show in the corresponding step of the tour.
is_selectize	Logical scalar indicating whether field corresponds to a selectize element.

Value

Character vector of length two. The first entry contains the element tag to identify the interface element to highlight, while the second entry contains the text.

Alternatively, NULL may be returned if .hideInterface(x, field) indicates that the corresponding interface element has been hidden.

Author(s)

Aaron Lun

---

Generate ggplot title and label instructions

Description

Generate ggplot title and label instructions

Usage

.buildLabs(
  x = NULL,
  y = NULL,
  color = NULL,
  shape = NULL,
  size = NULL,
  fill = NULL,
  group = NULL,
  title = NULL,
  subtitle = NULL
)

Arguments

x	The character label for the horizontal axis.
y	x The character label for the vertical axis.
color	The character title for the color scale legend.
shape	The character title for the point shape legend.
size	The character title for the point size legend.
fill	The character title for the color fill legend.
group	The character title for the group legend.
title	The character title for the plot title.
subtitle	The character title for the plot subtitle

Details

If any argument is NULL, the corresponding label is not set.

Value

Title and label instructions for ggplot as a character value.

Author(s)

Kevin Rue-Albrecht

Examples

cat(.buildLabs(y = "Title for Y axis", color = "Color label"))

---

Conditional elements on radio or checkbox selection

Description

Creates a conditional UI element that appears when the user picks a certain choice in a radio button, single checkbox or checkbox group interface element.

Usage

.conditionalOnRadio(id, choice, ...)

.conditionalOnCheckSolo(id, on_select = TRUE, ...)

.conditionalOnCheckGroup(id, choice, ...)

Arguments

id	String containing the ID of the UI element controlling the relevant choice.
choice	String containing the choice for the radio button or checkbox group on which to show the conditional element(s).
...	UI elements to show conditionally.
on_select	Logical scalar specifying whether the conditional element should be shown upon selection in a check box, or upon de-selection (if FALSE).

Details

These functions are just wrappers around conditionalPanel, with the added value coming from the pre-written conditional expressions in Javascript. They are useful for hiding elements that are only relevant when the right radio button or checkbox is selected. This means that we avoid cluttering the UI with options that are not immediately useful to the user.

Value

A HTML object containing interface elements in ... that only appear when the relevant condition is satisfied.

Author(s)

Aaron Lun

See Also

conditionalPanel, which is used under the hood.

---

Create observers for a modal for custom dimnames

Description

Create observers to launch a modal where users can input a list of custom row or column names. These observers register input changes in the app's memory and request an update to the affected panel.

Usage

.createCustomDimnamesModalObservers(
  plot_name,
  slot_name,
  button_name,
  se,
  input,
  session,
  pObjects,
  rObjects,
  source_type
)

Arguments

plot_name	String containing the name of the current panel.
slot_name	String specifying the slot of containing the names of the custom features. This will be modified by user interactions with the modal.
button_name	String containing the name of the button in the panel UI that launches the modal.
se	A SummarizedExperiment object after running .cacheCommonInfo.
input	The Shiny input object from the server function.
session	The Shiny session object from the server function.
pObjects	An environment containing global parameters generated in the iSEE app.
rObjects	A reactive list of values generated in the iSEE app.
source_type	String specifying the type of the panel that is source of the selection, either "row" or "column".

Details

This should be called in .createObservers for the target panel. It assumes that a button element with the suffix button_name is available in the UI (i.e., the full name is created by concatenated plot_name with button_name).

The modal UI provides options to sort the dimnames, validate them, clear the current text and import a selection from a specified row transmitter. These are all transient until “Apply” is clicked, at which point the app's memory is modified and an update is requested.

The custom names are stored in the slot_name as a single string with names separated by newlines. Hashes are treated as comments and any content after a hash is ignored when interpreting the names. Any leading and trailing whitespace is also ignored during interpretation.

Value

Observers are set up to launch the modal and monitor its UI elements. A NULL is invisibly returned.

Author(s)

Kevin Rue-Albrecht

---

Define parameter observers

Description

Define a series of observers to track “protected” or “unprotected” parameters for a given panel. These will register input changes to each specified parameter in the app's memory and request an update to the output of the affected panel.

Usage

.createUnprotectedParameterObservers(
  panel_name,
  fields,
  input,
  pObjects,
  rObjects,
  ignoreInit = TRUE,
  ignoreNULL = TRUE
)

.createProtectedParameterObservers(
  panel_name,
  fields,
  input,
  pObjects,
  rObjects,
  ignoreInit = TRUE,
  ignoreNULL = TRUE
)

Arguments

panel_name	String containing the name of the panel.
fields	Character vector of names of parameters for which to set up observers.
input	The Shiny input object from the server function.
pObjects	An environment containing global parameters generated in the iSEE app.
rObjects	A reactive list of values generated in the iSEE app.
ignoreInit, ignoreNULL	Further arguments to pass to observeEvent.

Details

A protected parameter is one that breaks existing multiple selections, e.g., by changing the actual data being plotted. Alterations to protected parameters will clear all active and saved selections in the panel, as those existing selections are assumed to not make any sense in the context of the modified output of that panel.

By comparison, an unprotected parameter only changes the aesthetics and will not clear existing selections.

Value

Observers are set up to monitor the UI elements that can change the protected and non-fundamental parameters. A NULL is invisibly returned.

Author(s)

Aaron Lun

See Also

.requestUpdate and .requestCleanUpdate, used to trigger updates to the panel output.

---

Extract assay submatrix

Description

Extract an assay submatrix based on the multiple row/column selection and any custom specifications from .createCustomDimnamesModalObservers.

Usage

.extractAssaySubmatrix(x, se, envir, use_custom_row_slot, custom_row_text_slot)

Arguments

x	A Panel instance that uses the row selection modal.
se	The current SummarizedExperiment object.
envir	The evaluation environment. This assumes that .processMultiSelections has already been run.
use_custom_row_slot	String specifying the name of the slot indicating whether to use custom rows.
custom_row_text_slot	String specifying the name of the slot holding the custom row names. This is expected to be of the same format as described in ?.createCustomDimnamesModalObservers.

Details

This is designed to extract a matrix of assay values for a subset of rows/columns of interest, most typically for a ComplexHeatmapPlot. It assumes that the class of x contains a slot indicating whether custom rows should be used, plus a slot to hold the selected custom row names (usually from a modal, see .createCustomDimnamesModalObservers).

If a multiple row selection is present in envir and custom rows are not to be used, that selection is used to define the rows of the submatrix. All columns are returned in the submatrix unless a multiple column selection is present in envir and the SelectEffect in x is “Restrict”, in which case only the selected columns are returned.

Value

A character vector of commands to set up the assay submatrix. The submatrix itself is generated within envir as the plot.data variable.

Author(s)

Kevin Rue-Albrecht

---

Get panel names

Description

Get panel names

Usage

.fullName(x)

.getEncodedName(x)

.getFullName(x)

Arguments

x	An instance of a Panel class.

Details

The encoded name is used internally as the name of various fields in input, output and reactive lists.

The full name is what should be shown in the interface and visible to the end-user.

Value

For .getEncodedName, a string containing the encoded panel name of x.

For .fullName, a string containing the full (plain-English) name of the class.

For .getFullName, a string containing the full name of x.

Author(s)

Aaron Lun

---

Get panel colors

Description

Functions to get/set panel colors at the user and developer level. This determines the color of the panel header as well as (for DotPlots) the color and fill of the brush.

Usage

.panelColor(x)

.getPanelColor(x)

Arguments

x	An instance of a Panel class.

Details

For developers: .panelColor is a method that should be subclassed for each Panel subclass. This determines the color theme for all instances of that class for use in, e.g., headers and box shadings. Developers should choose a color that is dark enough to serve as a background for white text. We recommend defining colors as hex color codes for full compatibility with both HTML elements and R plots.

For users: by default, .getPanelColor will return the default color of each panel as specified by the developer in .panelColor. However, users can override this by setting the panel.color global option to a named character vector of colors (see Examples). This can be used to customize the color scheme for any given call to iSEE. The names of the vector should be set to the name of class to be overridden; if a class is not named here, its default color is used.

Value

A string containing the color assigned to the class of x.

Author(s)

Aaron Lun

Examples

rdp <- ReducedDimensionPlot()

# Default color, as specified by the developer:
.panelColor(rdp)

# Still the default color:
.getPanelColor(rdp)

# Overriding the default colors:
sce <- SingleCellExperiment(list(logcounts=matrix(rnorm(1000), ncol=100)))
reducedDim(sce, "PCA") <- matrix(runif(200), ncol=2)

sce <- registerAppOptions(sce, panel.color=c(ReducedDimensionPlot="#1e90ff"))
if (interactive()) {
    iSEE(sce, initial=list(rdp))
}

---

Process multiple selections

Description

Generate and execute commands to process multiple selections, creating variables in the evaluation environment with the identity of the selected rows or columns.

Usage

.processMultiSelections(x, all_memory, all_contents, envir)

Arguments

x	An instance of a Panel class.
all_memory	A named list of Panel instances containing parameters for the current app state.
all_contents	A named list of arbitrary contents with one entry per panel.
envir	The evaluation environment. This is assumed to already contain se, the SummarizedExperiment object for the current dataset.

Details

This function is primarily intended for use by developers of new panels. It should be called inside .generateOutput to easily process row/column multiple selections. Developers can check whether row_selected or col_selected exists in envir to determine whether any row or column selection was performed (and adjust the behavior of .generateOutput accordingly).

Value

envir is populated with one, none or both of col_selected and/or row_selected, depending on whether x is receiving a multiple selection on the rows and/or columns. The return value is the character vector of commands required to construct those variables.

Author(s)

Aaron Lun

See Also

.generateOutput and its related generic .renderOutput, where this function should generally be used.

---

Remove invalid values in multiple choices

Description

Removes invalid values in a slot of a Panel object. This is usually called in .refineParameters.

Usage

.removeInvalidChoices(x, field, choices)

Arguments

x	An instance of a Panel class.
field	String containing the name of the relevant slot.
choices	Character vector of permissible values for this slot.

Value

x where the slot named field is replaced only with the values that exist in choices.

Author(s)

Kevin Rue-Albrecht

---

Replace with first choice

Description

Replace an NA or invalid value in a slot of a Panel object with the first valid choice. This is usually called in .refineParameters.

Usage

.replaceMissingWithFirst(x, field, choices)

Arguments

x	An instance of a Panel class.
field	String containing the name of the relevant slot.
choices	Character vector of permissible values for this slot.

Value

x where the slot named field is replaced with choices[1] if its value was previously NA or did not exist in choices.

Author(s)

Aaron Lun

---

Request Panel updates

Description

Request a re-rendering of the Panel output via reactive variables.

Usage

.requestUpdate(panel_name, rObjects)

.requestCleanUpdate(panel_name, pObjects, rObjects)

.requestActiveSelectionUpdate(
  panel_name,
  session,
  pObjects,
  rObjects,
  update_output = TRUE
)

Arguments

panel_name	String containing the panel name.
rObjects	A reactive list of values generated in the iSEE app.
pObjects	An environment containing global parameters generated in the iSEE app.
session	The Shiny session object from the server function.
update_output	A logical scalar indicating whether to call .requestUpdate as well.

Details

.requestUpdate should be used in various observers to request a re-rendering of the panel, usually in response to user-driven parameter changes in .createObservers.

.requestCleanUpdate is used for changes to protected parameters that invalidate existing multiple selections, e.g., if the coordinates change in a DotPlot, existing brushes and lassos are usually not applicable.

.requestActiveSelectionUpdate should be used in the observer expression that implements the panel's multiple selection mechanism.

Value

.requestUpdate will modify rObjects to request a re-rendering of the specified panel.

.requestCleanUpdate will also remove all active/saved selections in the chosen panel.

.requestActiveSelectionUpdate will modify rObjects to indicate that the active multiple selection for panel_name has changed. If update_output=TRUE, it will also request a re-rendering of the panel.

All functions will invisibly return NULL.

Author(s)

Aaron Lun

See Also

.createProtectedParameterObservers, for examples where the update-requesting functions are used.

---

Retrieve the panel output

Description

Retrieve the results of a previous .generateOutput call on this panel.

Usage

.retrieveOutput(panel_name, se, pObjects, rObjects)

Arguments

panel_name	String containing the panel name.
se	A SummarizedExperiment object containing the current dataset.
pObjects	An environment containing global parameters generated in the iSEE app.
rObjects	A reactive list of values generated in the iSEE app.

Details

This function should be used in the rendering expression in .renderOutput. It takes care of a number of house-keeping tasks required to satisfy .renderOutput's requirements, e.g., responding to .requestUpdate modifications to rObjects, setting the commands and contents and varname in pObjects.

This function will attempt to retrieve the cached output of .generateOutput if it was used elsewhere in the app. After retrieval, the cached value is wiped to ensure that it does not go stale. If no cached value is found, .generateOutput is called directly.

Value

The output of running .generateOutput for the current panel. Several fields in pObjects are also modified as a side-effect.

Author(s)

Aaron Lun

See Also

.renderOutput, where this function should be called.

.generateOutput, which is called by this function.

---

Set and get cached commons

Description

Get and set common cached information for each class. The setter should only ever be called in .cacheCommonInfo. The getter can be called anywhere but most usually in .defineInterface.

Usage

.setCachedCommonInfo(se, cls, ...)

.getCachedCommonInfo(se, cls)

Arguments

se	A SummarizedExperiment object containing the current dataset.
cls	String containing the name of the class for which this information is cached.
...	Any number of named R objects to cache.

Value

.setCachedCommonInfo returns se with ... added to its int_metadata.

.getCachedCommonInfo retrieves the cached common information for class cls.

Author(s)

Aaron Lun

See Also

?"cache-utils", for utilities to define some cached variables.

Examples

se <- SummarizedExperiment()
se <- .setCachedCommonInfo(se, "SomePanelClass",
    something=1, more_things=TRUE, something_else="A")
.getCachedCommonInfo(se, "SomePanelClass")

---

Generate ggplot aesthetic instructions

Description

Generate ggplot aesthetic instructions

Usage

.buildAes(
  x = TRUE,
  y = TRUE,
  color = FALSE,
  shape = FALSE,
  size = FALSE,
  fill = FALSE,
  group = FALSE,
  alt = NULL
)

Arguments

x	A logical that indicates whether to enable x in the aesthetic instructions (default: TRUE).
y	A logical that indicates whether to enable y in the aesthetic instructions (default: TRUE).
color	A logical that indicates whether to enable color in the aesthetic instructions (default: FALSE).
shape	A logical that indicates whether to enable shape in the aesthetic instructions (default: FALSE).
size	A logical that indicates whether to enable size in the aesthetic instructions (default: FALSE).
fill	A logical that indicates whether to enable fill in the aesthetic instructions (default: FALSE).
group	A logical that indicates whether to enable group in the aesthetic instructions (default: FALSE).
alt	Alternative aesthetics, supplied as a named character vector.

Value

Aesthetic instructions for ggplot as a character value.

Author(s)

Kevin Rue-Albrecht

Examples

.buildAes()

---

Caching utilities

Description

Utility functions to be used in a .cacheCommonInfo method, usually to identify names of elements of the SummarizedExperiment for later use in .defineInterface to populate the user interface.

Usage

.findAtomicFields(x)

.whichGroupable(x, max_levels = Inf)

.whichNumeric(x)

.isAssayNumeric(se, i)

Arguments

x	A data.frame or DataFrame, most typically the rowData or colData.
max_levels	Integer scalar specifying the maximum number unique values for x to be categorical.
se	The SummarizedExperiment object.
i	An integer scalar or string specifying the assay of interest in se.

Details

.findAtomicFields is necessary as many of the widgets used by iSEE (e.g., ggplot, datatable) do not know how to handle more complex types being stored as columns. Similarly, .whichNumeric and .whichGroupable can be used to specify options for visualization modes that only make sense for continuous or discrete variables respectively (e.g., sizing, faceting).

Value

For .findAtomicFields, a character vector of names of columns in x containing atomic R types.

For .whichNumeric, an integer vector containing the indices of the numeric columns.

For .whichGroupable, an integer vector containing the indices of the categorical columns.

For .isAssayNumeric, a logical scalar indicating whether the specified assay as numeric.

Author(s)

Aaron Lun, Kevin Rue-Albrecht, Charlotte Soneson

Examples

x <- DataFrame(
    A = rnorm(10),
    B = sample(letters, 10),
    DataFrame = I(DataFrame(
        C = rnorm(10),
        D = sample(letters, 10)
    ))
)

.findAtomicFields(x)
.whichGroupable(x)
.whichNumeric(x)

---

Check compatibility between ExperimentColorMap and SummarizedExperiment objects

Description

This function compares a pair of ExperimentColorMap and SingleCellExperiment objects, and examines whether all of the assays, colData, and rowData defined in the ExperimentColorMap object exist in the SingleCellExperiment object.

Usage

checkColormapCompatibility(ecm, se)

Arguments

ecm	An ExperimentColorMap.
se	A SingleCellExperiment.

Value

A character vector of incompatibility error messages, if any.

Author(s)

Kevin Rue-Albrecht

Examples

# Example colormaps ----

count_colors <- function(n){
  c("black","brown","red","orange","yellow")
}

qc_color_fun <- function(n){
  qc_colors <- c("forestgreen", "firebrick1")
  names(qc_colors) <- c("Y", "N")
  return(qc_colors)
}

ecm <- ExperimentColorMap(
    assays = list(
        tophat_counts = count_colors
    ),
    colData = list(
        passes_qc_checks_s = qc_color_fun
    )
)

# Example SingleCellExperiment ----

library(scRNAseq)
sce <- ReprocessedAllenData(assays="tophat_counts")

# Test for compatibility ----

checkColormapCompatibility(ecm, sce)

---

Set default slot values

Description

A utility function to set slots to default values if their values are not provided to initialize methods.

Usage

.emptyDefault(args, field, default)

Arguments

args	A named list of arguments to pass to the initialize method for a given class.
field	String specifying the field to set.
default	The default value of the slot in field.

Details

A more natural approach would be to have the default values in the arguments of the initialize method. However, this would require us to hard-code the slot names in the function signature, which would break our current DRY model of only specifying the slot names once.

Value

args is returned with the named field set to default if it was previously absent.

Author(s)

Aaron Lun, Kevin Rue-Albrecht

Examples

showMethods("initialize", classes = "ReducedDimensionPlot", includeDefs = TRUE)

---

Clean the dataset

Description

Clean the SummarizedExperiment by making sure that names of various fields are available and unique. Also transfer any information stored in rowRanges into rowData.

Usage

cleanDataset(se)

## S4 method for signature 'SummarizedExperiment'
cleanDataset(se)

## S4 method for signature 'SingleCellExperiment'
cleanDataset(se)

Arguments

se	A SummarizedExperiment object or one of its subclasses.

Details

Various Panels assume that the row and column names of the input SummarizedExperiment are available and unique. This function enforces that, adding consecutive integer names if not available and calling make.unique if they are duplicated.

Various Panels further assume that the assay, rowData, colData names are unique; if this is not the case, selectInput behaves in unexpected (and incorrect) ways. This function enforces that as well by running them through make.unique.

Finally, positional information in rowRanges is not accessible to iSEE. This function moves this information into rowData, prefixing the column names with rowRanges_.

For SingleCellExperiment object, we enforce uniqueness in the reducedDims.

All changes result in warnings as a “sensible” object is not expected to require any work.

Value

A cleaned version of se.

Author(s)

Aaron Lun, Charlotte Soneson

Examples

# Creating a very naughty SE.
se <- SummarizedExperiment(list(cbind(1:10, 2:11), cbind(2:11, 3:12)),
   colData=DataFrame(A=1:2, A=3:4, check.names=FALSE), 
   rowData=DataFrame(B=1:10, B=1:10, check.names=FALSE))
se

cleanDataset(se)

---

A collapsible box

Description

A custom collapsible box with Shiny inputs upon collapse, more or less stolen from shinyBS.

Usage

collapseBox(id, title, ..., open = FALSE, style = NULL)

Arguments

id	String specifying the identifier for this object, to use as a field of the Shiny input.
title	String specifying the title of the box for use in the UI.
...	Additional UI elements to show inside the box.
open	Logical scalar indicating whether this box should be open upon initialization.
style	String specifying the box style, defaults to "default".

Details

Collapsible boxes are used to hold parameters in the “parameter boxes” described in .defineInterface. It is recommended to format the id as PANEL_SLOT where PANEL is the name of the panel associated with the box and SLOT is the name of the slot that specifies whether this box should be open or not at initialization. (See Panel for some examples with DataBoxOpen.)

Do not confuse these boxes with the shinydashboard::boxes, which are used to hold the plot and table panels. Adding to the nomenclature confusion is the fact that our collapsible boxes are implemented in Javascript using the Bootstrap “panel” classes, which in turn has nothing to do with our Panel classes.

Value

A HTML tag object containing a collapsible box.

Comments on shinyBS

We would have preferred to use bsCollapse from shinyBS. However, that package does not seem to be under active maintenance, and there are several aspects that make it difficult to use. Specifically, it does not seem to behave well with conditional elements inside the box, and it also does needs a Depends: relationship with shinyBS.

For these reasons, we created our own collapsible box, taking code from shinyBS where appropriate. The underlying Javascript code for this object is present in inst/www and is attached to the search path for Shiny resources upon loading iSEE.

Author(s)

Aaron Lun

See Also

shinyBS, from which the Javascript code was derived.

.defineInterface, which should return a list of these collapsible boxes.

Examples

library(shiny)
collapseBox("SomePanelType1_ParamBoxOpen",
    title="Custom parameters",
    open=FALSE,
    selectInput("SomePanelType1_Thing",
        label="What thing?",
        choices=LETTERS, selected="A"
    )
)

---

The ColumnDataPlot panel

Description

The ColumnDataPlot is a panel class for creating a ColumnDotPlot where the y-axis represents a variable from the colData of a SummarizedExperiment object. It provides slots and methods for specifying which variable to use on the y-axis (and, optionally, also the x-axis), as well as a method to create the data.frame in preparation for plotting.

Slot overview

The following slots control the column data information that is used:

• YAxis, a string specifying the column of the colData to show on the y-axis. If NA, defaults to the first valid field (see ?".refineParameters,ColumnDotPlot-method").

• XAxis, string specifying what should be plotting on the x-axis. This can be any one of "None", "Column data" or "Column selection". Defaults to "None".

• XAxisColumnData, string specifying the column of the colData to show on the x-axis. If NA, defaults to the first valid field.

In addition, this class inherits all slots from its parent ColumnDotPlot, DotPlot and Panel classes.

Constructor

ColumnDataPlot(...) creates an instance of a ColumnDataPlot class, where any slot and its value can be passed to ... as a named argument.

Supported methods

In the following code snippets, x is an instance of a ColumnDataPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .refineParameters(x, se) returns x after replacing any NA value in YAxis or XAxisColumnData with the name of the first valid colData variable. This will also call the equivalent ColumnDotPlot method for further refinements to x. If no valid column metadata variables are available, NULL is returned instead.

For defining the interface:

• .defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.

• .panelColor(x) will return the specified default color for this panel class.

• .allowableXAxisChoices(x, se) returns a character vector specifying the acceptable variables in colData(se) that can be used as choices for the x-axis. This consists of all variables with atomic values.

• .allowableYAxisChoices(x, se) returns a character vector specifying the acceptable variables in colData(se) that can be used as choices for the y-axis. This consists of all variables with atomic values.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes. This will also call the equivalent ColumnDotPlot method.

For controlling selections:

• .multiSelectionInvalidated(x) returns TRUE if the x-axis uses multiple column selections, such that the point coordinates may change upon updates to upstream selections in transmitting panels. Otherwise, it dispatches to the ColumnDotPlot method.

For defining the panel name:

• .fullName(x) will return "Column data plot".

For creating the plot:

• .generateDotPlotData(x, envir) will create a data.frame of column metadata variables in envir. It will return the commands required to do so as well as a list of labels.

For documentation:

• .definePanelTour(x) returns an data.frame containing a panel-specific tour.

Subclass expectations

Subclasses do not have to provide any methods, as this is a concrete class.

Author(s)

Aaron Lun

See Also

ColumnDotPlot, for the immediate parent class.

Examples

#################
# For end-users #
#################

x <- ColumnDataPlot()
x[["XAxis"]]
x[["XAxis"]] <- "Column data"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)

old_cd <- colData(sce)
colData(sce) <- NULL

# Spits out a NULL and a warning if there is nothing to plot.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
colData(sce) <- old_cd
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

---

The ColumnDataTable panel

Description

The ColumnDataTable is a panel class for creating a ColumnTable where the value of the table is defined as the colData of the SummarizedExperiment. It provides functionality to extract the colData to coerce it into an appropriate data.frame in preparation for rendering.

Slot overview

This class inherits all slots from its parent ColumnTable and Table classes.

Constructor

ColumnDataTable(...) creates an instance of a ColumnDataTable class, where any slot and its value can be passed to ... as a named argument.

Note that ColSearch should be a character vector of length equal to the total number of columns in the colData, though only the entries for the atomic fields will actually be used.

Supported methods

In the following code snippets, x is an instance of a ColumnDataTable class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .cacheCommonInfo(x) adds a "ColumnDataTable" entry containing valid.colData.names, a character vector of names of atomic columns of the colData. This will also call the equivalent ColumnTable method.

• .refineParameters(x, se) adjusts ColSearch to a character vector of length equal to the number of atomic fields in the colData. This will also call the equivalent ColumnTable method for further refinements to x.

For defining the interface:

• .fullName(x) will return "Column data table".

• .panelColor(x) will return the specified default color for this panel class.

For creating the output:

• .generateTable(x, envir) will modify envir to contain the relevant data.frame for display, while returning a character vector of commands required to produce that data.frame. Each row of the data.frame should correspond to a column of the SummarizedExperiment.

For documentation:

• .definePanelTour(x) returns an data.frame containing the steps of a panel-specific tour.

Unless explicitly specialized above, all methods from the parent class Panel are also available.

Author(s)

Aaron Lun

Examples

#################
# For end-users #
#################

x <- ColumnDataTable()
x[["Selected"]]
x[["Selected"]] <- "SOME_SAMPLE_NAME"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()

# Search column refinement works as expected.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

---

The ColumnDotPlot virtual class

Description

The ColumnDotPlot is a virtual class where each column in the SummarizedExperiment is represented by no more than one point (i.e., a “dot”) in a brushable ggplot plot. It provides slots and methods to extract colData fields to control the per-point aesthetics on the plot. This panel will transmit column identities in both its single and multiple selections, and it can receive multiple column selections but not multiple row selections.

Slot overview

The following slots control coloring of the points:

• ColorByColumnData, a string specifying the colData field for controlling point color, if ColorBy="Column data" (see the Panel class). Defaults to the first valid field (see .cacheCommonInfo below).

• ColorByFeatureNameAssay, a string specifying the assay of the SummarizedExperiment object containing values to use for coloring, if ColorBy="Feature name". Defaults to "logcounts" in getPanelDefault, falling back to the name of the first valid assay (see ?".cacheCommonInfo,DotPlot-method" for the definition of validity).

• ColorBySampleNameColor, a string specifying the color to use for coloring an individual sample on the plot, if ColorBy="Sample name". Defaults to "red" in getPanelDefault.

The following slots control other metadata-related aesthetic aspects of the points:

• ShapeByColumnData, a string specifying the colData field for controlling point shape, if ShapeBy="Column data" (see the Panel class). The specified field should contain categorical values; defaults to the first such valid field.

• SizeByColumnData, a string specifying the colData field for controlling point size, if SizeBy="Column data" (see the Panel class). The specified field should contain continuous values; defaults to the first such valid field.

• TooltipColumnData, a character vector specifying colData fields to show in the tooltip. Defaults to 'character(0)', which displays only the 'colnames' value of the data point.

In addition, this class inherits all slots from its parent DotPlot and Panel classes.

Supported methods

In the following code snippets, x is an instance of a ColumnDotPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .cacheCommonInfo(x) adds a "ColumnDotPlot" entry containing valid.colData.names, a character vector of names of columns that are valid (i.e., contain atomic values); discrete.colData.names, a character vector of names for columns with discrete atomic values; and continuous.colData.names, a character vector of names of columns with continuous atomic values. This will also call the equivalent DotPlot method.

• .refineParameters(x, se) replaces NA values in ColorByFeatAssay with the first valid assay name in se. This will also call the equivalent DotPlot method.

For defining the interface:

• .hideInterface(x, field) returns a logical scalar indicating whether the interface element corresponding to field should be hidden. This returns TRUE for row selection parameters ("RowSelectionSource" and "RowSelectionRestrict"), otherwise it dispatches to the Panel method.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes. This will also call the equivalent DotPlot method.

For controlling selections:

• .multiSelectionRestricted(x) returns a logical scalar indicating whether x is restricting the plotted points to those that were selected in a transmitting panel.

• .multiSelectionDimension(x) returns "column" to indicate that a multiple column selection is being transmitted.

• .multiSelectionInvalidated(x) returns TRUE if the faceting options use multiple column selections, such that the point coordinates/domain may change upon updates to upstream selections in transmitting panels.

• .singleSelectionDimension(x) returns "sample" to indicate that a sample identity is being transmitted.

For documentation:

• .definePanelTour(x) returns an data.frame containing the steps of a tour relevant to subclasses, mostly tuning the more generic descriptions from the same method of the parent DotPlot.

• .getDotPlotColorHelp(x, color_choices) returns a data.frame containing the documentation for the "ColorBy" UI element, specialized for column-based dot plots.

Unless explicitly specialized above, all methods from the parent classes DotPlot and Panel are also available.

Subclass expectations

Subclasses are expected to implement methods for, at least:

• .generateDotPlotData

• .fullName

• .panelColor

The method for .generateDotPlotData should create a plot.data data.frame with one row per column in the SummarizedExperiment object.

Author(s)

Aaron Lun

See Also

DotPlot, for the immediate parent class that contains the actual slot definitions.

---

Define the selection colormap

Description

Define the colormap when coloring points in a DotPlot based on their assigned multiple row/column selection.

Usage

columnSelectionColorMap(x, levels)

rowSelectionColorMap(x, levels)

Arguments

x	An ExperimentColorMap object.
levels	Character vector containing the available levels of a ColorBy column derived from a series of multiple selections, usually generated by multiSelectionToFactor on the selection information in row_selected or col_selected.

Details

The "unselected" level is always assigned the grey color; colors for all other levels are generated by colDataColorMap(x) or rowDataColorMap(x). The "active" level is always assigned the first color from these functions, regardless of whether it is present in levels. This aims to provide some consistency in the coloring when the selections change.

Value

A named character vector of colors for each level in levels.

Author(s)

Aaron Lun

Examples

ecm <- ExperimentColorMap()
columnSelectionColorMap(ecm, c("active", "unselected"))
columnSelectionColorMap(ecm, c("active", "saved1", "unselected"))
columnSelectionColorMap(ecm, c("saved1", "unselected"))
columnSelectionColorMap(ecm, c("saved1"))

---

The ColumnTable class

Description

The ColumnTable is a virtual class where each column in the SummarizedExperiment is represented by no more than row in a datatable widget. In panels of this class, single and multiple selections can only be transmitted on the samples.

Slot overview

No new slots are added. All slots provided in the Table parent class are available.

Supported methods

In the following code snippets, x is an instance of a ColumnTable class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .refineParameters(x, se) replaces NA values in Selected with the first column name of se. This will also call the equivalent Table method.

For defining the interface:

• .hideInterface(x, field) returns a logical scalar indicating whether the interface element corresponding to field should be hidden. This returns TRUE for row selection parameters ("RowSelectionSource" and "RowSelectionRestrict"), otherwise it dispatches to the Panel method.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers to propagate changes in the Selected to linked plots. This will also call the equivalent Table method.

For controlling selections:

• .multiSelectionDimension(x) returns "column" to indicate that a column selection is being transmitted.

• .singleSelectionDimension(x) returns "sample" to indicate that a sample identity is being transmitted.

For rendering output:

• .showSelectionDetails(x) returns a HTML element containing details about the selected row. This requires a function to be registered by registerAppOptions under the option name "ColumnTable.select.details". The function should take a string containing the name of a feature (i.e., the current selection in the ColumnTable) and returns a HTML element. If no function is registered, NULL is returned.

Unless explicitly specialized above, all methods from the parent classes Table and Panel are also available.

Subclass expectations

Subclasses are expected to implement methods for:

• .generateTable

• .fullName

• .panelColor

The method for .generateTable should create a tab data.frame where each row corresponds to a column in the SummarizedExperiment object.

Author(s)

Aaron Lun

See Also

Table, for the immediate parent class that contains the actual slot definitions.

---

The ComplexHeatmapPlot panel

Description

The ComplexHeatmapPlot is a panel class for creating a Panel that displays an assay of a SummarizedExperiment object as a Heatmap with features as rows and samples and columns, respectively. It provides slots and methods for specifying the features of interest, which assay to display in the main heatmap, any transformations to perform on the data, and which metadata variables to display as row and column heatmap annotations.

ComplexHeatmapPlot slot overview

The following slots control the rows that are used:

• CustomRows, a logical scalar indicating whether the custom list of rows should be used. If FALSE, the incoming selection is used instead. Defaults to TRUE.

• CustomRowsText, string containing newline-separated row names. This specifies which rows of the SummarizedExperiment object are to be shown in the heatmap. If NA, defaults to the first row name of the SummarizedExperiment.

The following slots control the metadata variables that are used:

• ColumnData, a character vector specifying columns of the colData to show as columnAnnotation. Defaults to character(0).

• RowData, a character vector specifying columns of the rowData to show as rowAnnotation. Defaults to character(0).

• ShowColumnSelection, a logical vector indicating whether the column selection should be shown as an extra annotation bar. Defaults to TRUE.

• OrderColumnSelection, a logical vector indicating whether the column selection should be used to order columns in the heatmap. Defaults to TRUE.

The following slots control the choice of assay values:

• Assay, string specifying the name of the assay to use for obtaining expression values. Defaults to "logcounts" in getPanelDefault, falling back to the first valid assay name (see .cacheCommonInfo below).

The following slots control the clustering of rows:

• ClusterRows, a logical scalar indicating whether rows should be clustered by their assay values. Defaults to FALSE.

• ClusterRowsDistance, string specifying a distance measure to use. This can be any one of "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman", or "kendall". Defaults to "spearman".

• ClusterRowsMethod, string specifying a linkage method to use. This can be any one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", or "centroid". Defaults to "ward.D2".

The following control transformations applied to rows:

• AssayCenterRows is a logical scalar indicating whether assay values should be centered for each row.

• AssayScaleRows is a logical scalar indicating whether assay values should be scaled for each row. This transformation is only applicable if AssayCenterRows is TRUE.

The following slots control the color scale:

• CustomBounds is logical scale indicating whether the color scale should be constrained by an upper and/or a lower bounds.

• LowerBound is a numerical value setting the lower bound of the color scale; or NA to disable the lower bound when CustomBounds is TRUE.

• UpperBound is a numerical value setting the lower bound of the color scale; or NA to disable the upper bound when CustomBounds is TRUE.

• DivergentColormap is a character scalar indicating a 3-color divergent colormap to use when AssayCenterRows is TRUE.

The following slots refer to general plotting parameters:

• ShowDimNames, a character vector specifying the dimensions for which to display names. This can contain zero or more of "Rows" and "Columns". Defaults to "Rows".

• NamesRowFontSize, a numerical value setting the font size of the row names.

• NamesColumnFontSize, a numerical value setting the font size of the column names.

• LegendPosition, string specifying the position of the legend on the plot. Defaults to "Bottom" in getPanelDefault but can also be "Right".

• LegendDirection, string specifying the orientation of the legend on the plot for continuous covariates. Defaults to "Horizontal" in getPanelDefault but can also be "Vertical".

The following slots control some aspects of the user interface:

• DataBoxOpen, a logical scalar indicating whether the data parameter box should be open. Defaults to FALSE.

• VisualBoxOpen, a logical scalar indicating whether the visual parameter box should be open. Defaults to FALSE.

In addition, this class inherits all slots from its parent Panel class.

Constructor

ComplexHeatmapPlot(...) creates an instance of a ComplexHeatmapPlot class, where any slot and its value can be passed to ... as a named argument.

Supported methods

In the following code snippets, x is an instance of a ComplexHeatmapPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .cacheCommonInfo(x) adds a "ComplexHeatmapPlot" entry containing valid.assay.names, a character vector of valid (i.e., non-empty) assay names; discrete.assay.names, a character vector of valid assay names with discrete atomic values; continuous.assay.names, a character vector of valid assay names with continuous atomic values; valid.colData.names, a character vector of names of columns in colData that are valid; discrete.colData.names, a character vector of names for columns in colData with discrete atomic values; continuous.colData.names, a character vector of names of columns in colData with continuous atomic values; valid.rowData.names, a character vector of names of columns in rowData that are valid; discrete.rowData.names, a character vector of names for columns in rowData with discrete atomic values; continuous.rowData.names, a character vector of names of columns in rowData with continuous atomic values. Valid assay names are defined as those that are non-empty, i.e., not ""; valid columns in colData and rowData are defined as those that contain atomic values. This will also call the equivalent Panel method.

• .refineParameters(x, se) replaces any NA value in "Assay" with the first valid assay name; and NA value in "CustomRowsText" with the first row name. This will also call the equivalent Panel method for further refinements to x. If no valid column metadata fields are available, NULL is returned instead.

For defining the interface:

• .defineInterface(x, se, select_info) defines the user interface for manipulating all slots described above and in the parent classes. TODO It will also create a data parameter box that can respond to specialized .defineDataInterface, and a visual parameter box and a selection parameter box both specific to the ComplexHeatmapPlot panel. This will override the Panel method.

• .defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.

• .defineOutput(x) returns a UI element for a brushable plot.

• .panelColor(x) will return the specified default color for this panel class.

• .hideInterface(x, field) returns a logical scalar indicating whether the interface element corresponding to field should be hidden. This returns TRUE for the selection history ("SelectionHistory"), otherwise it dispatches to the Panel method.

For generating the output:

• .generateOutput(x, se, all_memory, all_contents) returns a list containing plot, a Heatmap object; commands, a list of character vector containing the R commands required to generate contents and plot; and contents and varname, both set to NULL as this is not a transmitting panel.

• .exportOutput(x, se, all_memory, all_contents) will create a PDF file containing the current plot, and return a string containing the path to that PDF. This assumes that the plot field returned by .generateOutput is a Heatmap object.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes. This will also call the equivalent Panel method.

• .renderOutput(x, se, output, pObjects, rObjects) will add a rendered plot element to output. The reactive expression will add the contents of the plot to pObjects$contents and the relevant commands to pObjects$commands. This will also call the equivalent Panel method to render the panel information text boxes.

For defining the panel name:

• .fullName(x) will return "Complex heatmap".

For documentation:

• .definePanelTour(x) returns an data.frame containing a panel-specific tour.

Author(s)

Kevin Rue-Albrecht

See Also

Panel, for the immediate parent class.

Examples

#################
# For end-users #
#################

x <- ComplexHeatmapPlot()
x[["ShowDimNames"]]
x[["ShowDimNames"]] <- c("Rows", "Columns")

##################
# For developers #
##################

library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)

old_cd <- colData(sce)
colData(sce) <- NULL

# Spits out a NULL and a warning if there is nothing to plot.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
colData(sce) <- old_cd
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

---

Constants

Description

Constant values used throughout iSEE panels and extensions.

Panel slot names

.dataParamBoxOpen

Name of slot that indicates whether the 'Data parameter' box is open.

.multiSelectHistory

Name of slot that stores the list of saved selections.

.organizationHeight

Name of slot that stores the panel height.

.organizationWidth

Name of slot that stores the panel width.

Multiple selection parameters

.noSelection

Value displayed in the absence of selection.

Author(s)

Kevin Rue-Albrecht

---

Create custom panels

Description

Helper functions for quick-and-dirty creation of custom panels, usually in the context of a one-off application. This creates a new class with specialized methods for showing content based on a user-specified function.

Usage

createCustomTable(
  FUN,
  restrict = NULL,
  className = "CustomTable",
  fullName = "Custom table",
  FUN.selection.details = NULL,
  where = topenv(parent.frame())
)

createCustomPlot(
  FUN,
  restrict = NULL,
  className = "CustomPlot",
  fullName = "Custom plot",
  where = topenv(parent.frame())
)

Arguments

FUN	A function that generates a data.frame or a ggplot, for createCustomTable and createCustomPlot respectively. See Details for the expected arguments.
restrict	Character vector of names of optional arguments in FUN to which the UI is restricted. If specified, only the listed arguments receive UI elements in the interface.
className	String containing the name of the new Panel class.
fullName	String containing the full name of the new class.
FUN.selection.details	Function generating a UI element that displays details about the current selection, if any.
where	An environment indicating where the class and method definitions should be stored.

Details

FUN is expected to have the following first 3 arguments:

• se, a SummarizedExperiment object for the current dataset of interest.

• rows, a list of row selections received from the transmitting panel. This contains one or more character vectors of row names in active and saved selections. Alternatively, this may be NULL if no selection has been made in the transmitter.

• columns, a list of column selections received from the transmitting panel. This contains one or more character vectors of column names in active and saved selections. Alternatively, this may be NULL if no selection has been made in the transmitter.

Any number of additional named arguments may also be present in FUN. All such arguments should have default values, as these are used to automatically generate UI elements in the panel:

• Character vectors will get a selectInput.

• Strings will get a textInput.

• Numeric scalars will get a numericInput.

• Logical scalars will get a checkboxInput.

Arguments with other types of default values are ignored. If restrict is specified, arguments will only have corresponding UI elements if they are listed in restrict. All user interactions with these elements will automatically trigger regeneration of the panel contents.

Classes created via these functions are extremely limited. Only scalar inputs are supported via the UI and all panels cannot transmit to the rest of the app. We recommend only using these functions for one-off applications to quickly prototype concepts; serious Panel extensions should be done explicitly.

Value

A new class and its methods are defined in the global environment. A generator function for creating new instances of the class is returned.

Author(s)

Aaron Lun

Examples

library(scater)
CUSTOM_DIMRED <- function(se, rows, columns, ntop=500, scale=TRUE,
    mode=c("PCA", "TSNE", "UMAP"))
{
    if (is.null(columns)) {
        return(
            ggplot() + theme_void() + geom_text(
                aes(x, y, label=label),
                data.frame(x=0, y=0, label="No column data selected."),
                size=5)
            )
    }

    mode <- match.arg(mode)
    if (mode=="PCA") {
        calcFUN <- runPCA
    } else if (mode=="TSNE") {
        calcFUN <- runTSNE
    } else if (mode=="UMAP") {
        calcFUN <- runUMAP
    }

    kept <- se[, unique(unlist(columns))]
    kept <- calcFUN(kept, ncomponents=2, ntop=ntop,
        scale=scale, subset_row=unique(unlist(rows)))
    plotReducedDim(kept, mode)
}

GEN <- createCustomPlot(CUSTOM_DIMRED)
GEN()

if (interactive()) {
    library(scRNAseq)
    sce <- ReprocessedAllenData("tophat_counts")
    library(scater)
    sce <- logNormCounts(sce, exprs_values="tophat_counts")

    iSEE(sce, initial=list(
        ColumnDataPlot(PanelId=1L),
        GEN(ColumnSelectionSource="ColumnDataPlot1")
    ))
}

---

Create a landing page

Description

Define a function to create a landing page in which users can specify or upload SummarizedExperiment objects.

Usage

createLandingPage(
  seUI = NULL,
  seLoad = NULL,
  initUI = NULL,
  initLoad = NULL,
  requireButton = TRUE
)

Arguments

seUI	Function that accepts a single id argument and returns a UI element for specifying the SummarizedExperiment.
seLoad	Function that accepts the input value of the UI element from seUI and returns a SummarizedExperiment object.
initUI	Function that accepts a single id argument and returns a UI element for specifying the initial state.
initLoad	Function that accepts the input value of the UI element from initUI and returns a list of Panels.
requireButton	Logical scalar indicating whether the app should require an explicit button press to initialize, or if it should initialize upon any modification to the UI element in seUI.

Details

By default, this function creates a landing page in which users can upload an RDS file containing a SummarizedExperiment, which is subsequently read by readRDS to launch an instance of iSEE. However, any source of SummarizedExperiment objects can be used; for example, we can retrieve them from databases by modifying seUI and seLoad appropriately.

The default landing page also allows users to upload a RDS file containing a list of Panels that specifies the initial state of the iSEE instance (to be used as the initial argument in iSEE). Again, any source can be used to create this list if initUI and initLoad are modified appropriately.

The UI elements for the SummarizedExperiment and the initial state are named "se" and "initial" respectively. This can be used in Shiny bookmarking to initialize an iSEE in a desired state by simply clicking a link, provided that requireButton=FALSE so that reactive expressions are immediately triggered upon setting se= and initial= in the URL. We do not use bookmarking to set all individual iSEE parameters as we will run afoul of URL character limits.

Value

A function that generates a landing page upon being passed to iSEE as the landingPage argument.

Defining a custom landing page

We note that createLandingPage is just a limited wrapper around the landing page API. In iSEE, landingPage can be any function that accepts the following arguments:

• FUN, a function to initialize the iSEE observer architecture. This function expects to be passed:

  • SE, a SummarizedExperiment object.

  • INITIAL, a list of Panel objects describing the initial application state. If NULL, the initial state from initial in the top-level iSEE call is used instead.

  • TOUR, a data.frame containing a tour to be attached to the app - see defaultTour for an example. If NULL (the default), no tour is added.

  • COLORMAP, an ExperimentColorMap object that defines the colormaps to use in the application.

• input, the Shiny input list.

• output, the Shiny output list.

• session, the Shiny session object.

The landingPage function should define a renderUI expression that is assigned to output$allPanels. This should define a UI that contains all widgets necessary for a user to set up an iSEE session interactively. We suggest that all UI elements have IDs prefixed with "initialize_INTERNAL" to avoid conflicts.

The function should also define observers to respond to user interactions with the UI elements. These are typically used to define a SummarizedExperiment object and an input state as a list of Panels; any one of these observers may then call FUN on those arguments to launch the main iSEE instance.

Note that, once the main app is launched, the UI elements constructed here are lost and observers will never be called again. There is no explicit “unload” mechanism to return to the landing page from the main app, though a browser refresh is usually sufficient.

Author(s)

Aaron Lun

Examples

createLandingPage()

# Alternative approach, to create a landing page
# that opens one of the datasets from the scRNAseq package.
library(scRNAseq)
all.data <- ls("package:scRNAseq")
all.data <- all.data[grep("Data$", all.data)]

lpfun <- createLandingPage(
    seUI=function(id) selectInput(id, "Dataset:", choices=all.data),
    seLoad=function(x) get(x, as.environment("package:scRNAseq"))()
)

app <- iSEE(landingPage=lpfun)
if (interactive()) {
  shiny::runApp(app, port=1234)
}

---

Define the default tour

Description

Define the default tour for the subset of the Allen brain dataset. This is only available when run on the iSEE(sce) example in ?"iSEE".

Usage

defaultTour()

Value

A data.frame where each row is a tour step. The first column specifies the UI element to be highlighted by the tour, while the second column contains the tour text.

Author(s)

Aaron Lun

Examples

defaultTour()

---

Documentation generics

Description

The generics power the creation of panel-specific documentation within the iSEE app. Users can click on an icon next to the panel name to open a self-guided tour for that panel's functionality.

Defining the panel tour

.definePanelTour(x) takes a Panel x and is expected to return a data.frame with the character fields "element" and "intro". Each row corresponds to a step of an rintrojs tour; the "element" specifies the active UI element to be highlighted in that step, while the "intro" element contains the HTML-formatted text to show in the tour pop-up.

It is a good idea to callNextMethod() to obtain the tour steps for the parent class to append onto the current class's data.frame. In some cases, modification of the parent class's tour steps may be necessary if some of the parent's functionality has been overwritten. Some communication with the parent's maintainers may be necessary to establish a stable way to identify the rows corresponding to the steps to be written, e.g., based on the row names of the data.frame.

A tour for a Panel x is expected to only highlight UI elements on the same panel. This is very important as other panels cannot be assumed to exist in an arbitrary instance of iSEE. As such, these tours are not well-suited to highlighting interactions between different panels.

The observer set-up for the panel tour is done in .createObservers for the base Panel class. No further action is required on behalf of developers to set up the triggers to launch the tour.

Defining UI-specific tours

It is possible to provide tours for individual UI elements, which can be more helpful than a single large tour for the entire panel. A documented element has a clickable icon (usually generated by functions like .selectInput.iSEE) that launches a specific tour, typically explaining the behavior and effects of the associated parameter. The tours themselves should be registered by .addSpecificTour. This is best done inside the various interface-defining functions (e.g., .defineInterface and related methods) where the documentation can be written adjacent to the definition of the UI element itself.

For a DotPlot instance x, the .getDotPlotColorHelp(x, color_choices) generic should return a function that returns a data.frame containing the rintrojs tour for the color choice UI element, i.e., "ColorBy". This allows downstream Panels to tune the wording of the color documentation, given that this is commonly specialized. color_choices is a character vector that contains the valid choices for the "ColorBy" radio button; some input datasets will not have, e.g., any column data, so the corresponding button will not be shown and its associated tour can be omitted.

Author(s)

Aaron Lun

---

The DotPlot virtual class

Description

The DotPlot is a virtual class for all panels where each row or column in the SummarizedExperiment is represented by no more than one point (i.e., a “dot”) in a brushable ggplot plot. It provides slots and methods to create the plot, to control various aesthetics of the dots, and to store the brush or lasso selection.

Slot overview

The following slots are relevant to coloring of the points:

• ColorBy, a string specifying how points should be colored. This should be one of "None", "Feature name", "Sample name" and either "Column data" (for ColumnDotPlots) or "Row data" (for RowDotPlots). Defaults to "None".

• ColorByDefaultColor, a string specifying the default color to use for all points if ColorBy="None". Defaults to "black" in getPanelDefault.

• ColorByFeatureName, a string specifying the feature to be used for coloring points when ColorBy="Feature name". For RowDotPlots, this is used to highlight the point corresponding to the selected feature; for ColumnDotPlots, this is used to color each point according to the expression of that feature. If NA, this defaults to the name of the first row.

• ColorByFeatureSource, a string specifying the name of the panel to use for transmitting the feature selection to ColorByFeatureName. Defaults to "---".

• ColorBySampleName, a string specifying the sample to be used for coloring points when ColorBy="Sample name". For RowDotPlots, this is used to color each point according to the expression of that sample; for ColumnDotPlots, this is used to highlight the point corresponding to the selected sample. If NA, this defaults to the name of the first column.

• ColorBySampleSource, a string specifying the name of the panel to use for transmitting the sample selection to ColorBySampleNameColor. Defaults to "---".

• ColorByFeatureDynamicSource, a logical scalar indicating whether x should dynamically change its selection source when coloring by feature. Defaults to FALSE in getPanelDefault.

• ColorBySampleDynamicSource, a logical scalar indicating whether x should dynamically change its selection source when coloring by feature. Defaults to FALSE in getPanelDefault.

• SelectionAlpha, a numeric scalar in [0, 1] specifying the transparency to use for non-selected points. Defaults to 0.1 in getPanelDefault.

The following slots control other metadata-related aesthetic aspects of the points:

• ShapeBy, a string specifying how the point shape should be determined. This should be one of "None" and either "Column data" (for ColumnDotPlots) or "Row data" (for RowDotPlots). Defaults to "None".

• SizeBy, a string specifying the metadata field for controlling point size. This should be one of "None" and either "Column data" (for ColumnDotPlots) or "Row data" (for RowDotPlots). Defaults to "None".

The following slots control the faceting:

• FacetRowBy, a string indicating what to use for creating row facets. For RowDotPlots, this should be one of "None", "Row data" or "Row selection". For ColumnDotPlots, this should be one of "None", "Column data" or "Column selection". Defaults to "None", i.e., no row faceting.

• FacetByColumn, a string indicating what to use for creating column facets. For RowDotPlots, this should be one of "None", "Row data" or "Row selection". For ColumnDotPlots, this should be one of "None", "Column data" or "Column selection". Defaults to "None", i.e., no column faceting.

The following slots control any text to be shown on the plot:

• LabelCenters, a logical scalar indicating whether the label the centers (technically medoids) of all cells in each group, where groups are defined by a discrete covariate in the relevant metadata field. Defaults to FALSE.

• LabelCentersBy, a string specifying the metadata field to define the groups when LabelCenters is TRUE. This should be a discrete variable in rowData or colData for RowDotPlots and ColumnDotPlots, respectively. Defaults to the name of the first column.

• LabelCentersColor, a string specifying the color used for the labels at the center of each group. Only used when LabelCenters is TRUE. Defaults to "black".

• CustomLabels, a logical scalar indicating whether custom labels should be inserted on specific points. Defaults to FALSE.

• CustomLabelsText, a (possibly multi-line) string with the names of the points to label when CustomLabels is set to TRUE. Each line should contain the name of a row or column for RowDotPlots and ColumnDotPlots, respectively. Leading and trailing whitespace are stripped, and all text on a line after # is ignored. Defaults to the name of the first row/column.

The following slots control interactions with the plot image:

• ZoomData, a named numeric vector of plot coordinates with "xmin", "xmax", "ymin" and "ymax" elements parameterizing the zoom boundaries. Defaults to an empty vector, i.e., no zoom.

• BrushData, a list containing either a Shiny brush (see ?brushedPoints) or an iSEE lasso (see ?lassoPoints). Defaults to an empty list, i.e., no brush or lasso.

• HoverInfo, a logical scalar indicating whether the feature/sample name should be shown upon mouse-over of the point. Defaults to TRUE.

The following slots control some aspects of the user interface:

• DataBoxOpen, a logical scalar indicating whether the data parameter box should be open. Defaults to FALSE.

• VisualBoxOpen, a logical scalar indicating whether the visual parameter box should be open. Defaults to FALSE.

• VisualChoices, a character vector specifying the visible interface elements upon initialization. This can contain zero or more of "Color", "Shape", "Size", "Point" , "Facet", "Text", and "Other". Defaults to "Color".

The following slots control the addition of a contour:

• ContourAdd, logical scalar indicating whether a contour should be added to a (scatter) plot. Defaults to FALSE.

• ContourColor, string specifying the color to use for the contour lines. Defaults to "blue".

The following slot controls whether the aspect ratio is fixed to 1 or not:

• FixAspectRatio, logical scalar indicating whether the aspect ratio of a scatter plot should be fixed to 1. Defaults to FALSE.

The following slot controls whether the violin boundaries are plotted or not:

• ViolinAdd, logical scalar indicating whether the violin boundaries should be plotted. Defaults to TRUE.

The following slots control the general appearance of the points.

• PointSize, positive numeric scalar specifying the relative size of the points. Defaults to 1.

• PointAlpha, non-negative numeric scalar specifying the transparency of the points. Defaults to 1, i.e., not transparent.

• Downsample, logical scalar indicating whether to downsample points for faster plotting. Defaults to FALSE in getPanelDefault.

• DownsampleResolution, numeric scalar specifying the resolution of the downsampling grid (see ?subsetPointsByGrid) if Downsample=TRUE. Larger values correspond to reduced downsampling at the cost of plotting speed. Defaults to 200 in getPanelDefault.

The following slots refer to general plotting parameters:

• FontSize, positive numeric scalar specifying the relative font size. Defaults to 1 in getPanelDefault.

• PointSize, positive numeric scalar specifying the relative point size. Defaults to 1 in getPanelDefault.

• LegendPosition, string specifying the position of the legend on the plot. Defaults to "Bottom" in getPanelDefault. The other valid choice is "Right".

In addition, this class inherits all slots from its parent Panel class.

Supported methods

In the following code snippets, x is an instance of a DotPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up the objects:

• .cacheCommonInfo(x) adds a "DotPlot" entry containing valid.assay.names, a character vector of valid assay names. Valid names are defined as those that are non-empty, i.e., not "". This method will also call the equivalent Panel method.

• .refineParameters(x, se) replaces NA values in ColorByFeatureName and ColorBySampleNameColor with the first row and column name, respectively, of se. This will also call the equivalent Panel method.

For defining the interface:

• .defineInterface(x, se, select_info) defines the user interface for manipulating all slots described above and in the parent classes. It will also create a data parameter box that can respond to specialized .defineDataInterface. This will override the Panel method.

• .defineVisualColorInterface(x, se, select_info) defines the user interface subpanel for manipulating the color of the points.

• .defineVisualShapeInterface(x, se) defines the user interface subpanel for manipulating the shape of the points.

• .defineVisualSizeInterface(x, se) defines the user interface subpanel for manipulating the size of the points.

• .defineVisualPointInterface(x, se) defines the user interface subpanel for manipulating other point-related parameters.

• .defineVisualFacetInterface(x, se) defines the user interface subpanel for manipulating facet-related parameters.

• .defineVisualTextInterface(x, se) defines the user interface subpanel for manipulating text-related parameters.

• .defineVisualOtherInterface(x, se) defines the user interface subpanel for manipulating other parameters. Currently this returns NULL.

• .defineOutput(x) returns a UI element for a brushable plot.

• .allowableColorByDataChoices(x, se) returns a character vector containing all atomic variables in the relevant *Data dimension.

For generating the output:

• .generateOutput(x, se, all_memory, all_contents) returns a list containing contents, a data.frame with one row per point currently present in the plot; plot, a ggplot object; commands, a list of character vector containing the R commands required to generate contents and plot; and varname, a string containing the name of the variable in commands that was used to obtain contents.

• .generateDotPlot(x, labels, envir) returns a list containing plot and commands, as described above. This is called within .generateOutput for all DotPlot instances by default. Methods are also guaranteed to generate a dot.plot variable in envir containing the ggplot object corresponding to plot.

• .prioritizeDotPlotData(x, envir) returns NULL.

• .colorByNoneDotPlotField(x) returns NULL.

• .colorByNoneDotPlotScale(x) returns NULL.

• .exportOutput(x, se, all_memory, all_contents) will create a PDF file containing the current plot, and return a string containing the path to that PDF. This assumes that the plot field returned by .generateOutput is a ggplot object.

For defining reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for some (but not all!) of the slots. This will also call the equivalent Panel method.

• .renderOutput(x, se, output, pObjects, rObjects) will add a rendered plot element to output. The reactive expression will add the contents of the plot to pObjects$contents and the relevant commands to pObjects$commands. This will also call the equivalent Panel method to render the panel information text boxes.

For controlling selections:

• .multiSelectionCommands(x, index) returns a character vector of R expressions that - when evaluated - returns a character vector of the names of selected points in the active and/or saved selections of x. The active selection is returned if index=NA, otherwise one of the saved selection is returned.

• .multiSelectionActive(x) returns x[["BrushData"]] or NULL if there is no brush or closed lasso.

• .multiSelectionClear(x) returns x after setting the BrushData slot to an empty list.

• .singleSelectionValue(x, contents) returns the name of the first selected element in the active brush. If no brush is active, NULL is returned instead.

• .singleSelectionSlots(x) will return a list specifying the slots that can be updated by single selections in transmitter panels, mostly related to the choice of coloring parameters. This includes the output of callNextMethod.

For documentation:

• .definePanelTour(x) returns an data.frame containing the steps of a tour relevant to subclasses, mostly describing the specification of visual effects and the creation of a brush or lasso.

Unless explicitly specialized above, all methods from the parent class Panel are also available.

Subclass expectations

The DotPlot is a rather vaguely defined class for which the only purpose is to avoid duplicating code for ColumnDotPlots and RowDotPlots. We recommend extending those subclasses instead.

Author(s)

Aaron Lun

See Also

RowDotPlot and ColumnDotPlot, which are more amenable to extension.

---

ExperimentColorMap class

Description

ExperimentColorMap class

Usage

ExperimentColorMap(
  assays = list(),
  colData = list(),
  rowData = list(),
  all_discrete = list(assays = NULL, colData = NULL, rowData = NULL),
  all_continuous = list(assays = NULL, colData = NULL, rowData = NULL),
  global_discrete = NULL,
  global_continuous = NULL,
  ...
)

Arguments

assays	List of colormaps for assays.
colData	List of colormaps for colData.
rowData	List of colormaps for rowData.
all_discrete	Colormaps applied to all undefined categorical assays, colData, and rowData, respectively.
all_continuous	Colormaps applied to all undefined continuous assays, colData, and rowData, respectively.
global_discrete	Colormap applied to all undefined categorical covariates.
global_continuous	Colormap applied to all undefined continuous covariates.
...	additional arguments passed on to the ExperimentColorMap constructor

Details

Colormaps must all be functions that take at least one argument: the number of (named) colours to return as a character vector. This argument may be ignored in the body of the colormap function to produce constant colormaps.

Value

An object of class ExperimentColorMap

Categorical colormaps

The default categorical colormap emulates the default ggplot2 categorical color palette (Credit: https://stackoverflow.com/questions/8197559/emulate-ggplot2-default-color-palette). This palette returns a set of colors sampled in steps of equal size that correspond to approximately equal perceptual changes in color:

function(n) {
    hues=seq(15, 375, length=(n + 1))
    hcl(h=hues, l=65, c=100)[seq_len(n)]
}

To change the palette for all categorical variables, users must supply a colormap that returns a similar value; namely, an unnamed character vector of length n. For instance, using the base R palette rainbow.colors

function(n) {
    rainbow(n)
}

Accessors

In the following code snippets, x is an ExperimentColorMap object.

assayColorMap(x, i, ..., discrete=FALSE):

Get an assays colormap for the specified assay i.

colDataColorMap(x, i, ..., discrete=FALSE):

Get a colData colormap for the specified colData column i.

rowDataColorMap(x, i, ..., discrete=FALSE):

Get a rowData colormap for the specified rowData column i.

If the colormap for i cannot be found, one of the default colormaps is returned. In this case, discrete is a logical scalar that indicates whether the colormap should be categorical. The more specialized default is first attempted - e.g., for assayColorMap, this would be the assay colormap specified in assays of all_discrete or all_continuous - before falling back to the global default in global_discrete or global_continuous. Similarly, if i is missing, the default discrete/continuous colormap is returned.

Setters

In the following code snippets, x is an ExperimentColorMap object, and i is a character or numeric index.

assayColorMap(x, i, ...) <- value:

Set an assays colormap.

colDataColorMap(x, i, ...) <- value:

Set a colData colormap.

rowDataColorMap(x, i, ...) <- value:

Set a rowData colormap.

assay(x, i, ...) <- value:

Alias. Set an assays colormap.

Examples

# Example colormaps ----

count_colors <- function(n){
  c("black", "brown", "red", "orange", "yellow")
}
fpkm_colors <- viridis::inferno
tpm_colors <- viridis::plasma

qc_color_fun <- function(n){
  qc_colors <- c("forestgreen", "firebrick1")
  names(qc_colors) <- c("Y", "N")
  return(qc_colors)
}

# Constructor ----

ecm <- ExperimentColorMap(
    assays=list(
        counts=count_colors,
        tophat_counts=count_colors,
        cufflinks_fpkm=fpkm_colors,
        rsem_tpm=tpm_colors
    ),
    colData=list(
        passes_qc_checks_s=qc_color_fun
    )
)

# Accessors ----

# assay colormaps
assayColorMap(ecm, "logcounts") # [undefined --> default]
assayColorMap(ecm, "counts")
assayColorMap(ecm, "cufflinks_fpkm")
assay(ecm, "cufflinks_fpkm") # alias

# colData colormaps
colDataColorMap(ecm, "passes_qc_checks_s")
colDataColorMap(ecm, "undefined")

# rowData colormaps
rowDataColorMap(ecm, "undefined")

# generic accessors
assays(ecm)
assayNames(ecm)

# Setters ----

assayColorMap(ecm, "counts") <- function(n){c("blue", "white", "red")}
assay(ecm, 1) <- function(n){c("blue", "white", "red")}

colDataColorMap(ecm, "passes_qc_checks_s") <- function(n){NULL}
rowDataColorMap(ecm, "undefined") <- function(n){NULL}

# Categorical colormaps ----

# Override all discrete colormaps using the base rainbow palette
ecm <- ExperimentColorMap(global_discrete = rainbow)
n <- 10
plot(1:n, col=assayColorMap(ecm, "undefined", discrete = TRUE)(n), pch=20, cex=3)

---

The FeatureAssayPlot panel

Description

The FeatureAssayPlot is a panel class for creating a ColumnDotPlot where the y-axis represents the expression of a feature of interest, using the assay values of the SummarizedExperiment. It provides slots and methods to specify the feature and what to plot on the x-axis, as well as a method to actually create a data.frame containing those pieces of data in preparation for plotting.

Slot overview

The following slots control the values on the y-axis:

• YAxisFeatureName, a string specifying the name of the feature to plot on the y-axis. If NA, defaults to the first row name of the SummarizedExperiment object.

• Assay, string specifying the name of the assay to use for obtaining expression values. Defaults to "logcounts" in getPanelDefault, falling back to the name of the first valid assay (see ?".cacheCommonInfo,DotPlot-method" for the definition of validity).

• YAxisFeatureSource, string specifying the encoded name of the transmitting panel to obtain a single selection that replaces YAxisFeatureName. Defaults to "---", i.e., no transmission is performed.

• YAxisFeatureDynamicSource, a logical scalar indicating whether x should dynamically change its selection source for the y-axis. Defaults to FALSE in getPanelDefault.

The following slots control the values on the x-axis:

• XAxis, string specifying what should be plotting on the x-axis. This can be any one of "None", "Feature name", "Column data" or "Column selection". Defaults to "None".

• XAxisColumnData, string specifying which column of the colData should be shown on the x-axis, if XAxis="Column data". Defaults to the first valid colData field (see ?".refineParameters,ColumnDotPlot-method" for details).

• XAaxisFeatureName, string specifying the name of the feature to plot on the x-axis, if XAxis="Feature name". Defaults to the first row name.

• XAxisFeatureSource, string specifying the encoded name of the transmitting panel to obtain a single selection that replaces XAxisFeatureName. Defaults to "---", i.e., no transmission is performed.

• XAxisFeatureDynamicSource, a logical scalar indicating whether x should dynamically change its selection source for the x-axis. Defaults to FALSE in getPanelDefault.

In addition, this class inherits all slots from its parent ColumnDotPlot, DotPlot and Panel classes.

Constructor

FeatureAssayPlot(...) creates an instance of a FeatureAssayPlot class, where any slot and its value can be passed to ... as a named argument.

Supported methods

In the following code snippets, x is an instance of a FeatureAssayPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .refineParameters(x, se) replaces any NA values in XAxisFeatureName and YAxisFeatureName with the first row name; any NA value in Assay with the first valid assay name; and any NA value in XAxisColumnData with the first valid column metadata field. This will also call the equivalent ColumnDotPlot method for further refinements to x. If no rows or assays are present, NULL is returned instead.

For defining the interface:

• .defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.

• .panelColor(x) will return the specified default color for this panel class.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes. This will also call the equivalent ColumnDotPlot method.

For defining the panel name:

• .fullName(x) will return "Feature assay plot".

For creating the plot:

• .generateDotPlotData(x, envir) will create a data.frame of feature expression values in envir. It will return the commands required to do so as well as a list of labels.

For managing selections:

• .singleSelectionSlots(x) will return a list specifying the slots that can be updated by single selections in transmitter panels, mostly related to the choice of feature on the x- and y-axes. This includes the output of the method for the parent ColumnDotPlot class.

• .multiSelectionInvalidated(x) returns TRUE if the x-axis uses multiple column selections, such that the point coordinates may change upon updates to upstream selections in transmitting panels. Otherwise, it dispatches to the ColumnDotPlot method.

For documentation:

• .definePanelTour(x) returns an data.frame containing a panel-specific tour.

Author(s)

Aaron Lun

See Also

ColumnDotPlot, for the immediate parent class.

Examples

#################
# For end-users #
#################

x <- FeatureAssayPlot()
x[["XAxis"]]
x[["Assay"]] <- "logcounts"
x[["XAxisColumnData"]] <- "stuff"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)

old_assay_names <- assayNames(sce)
assayNames(sce) <- character(length(old_assay_names))

# Spits out a NULL and a warning if no assays are named.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
assayNames(sce) <- old_assay_names
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

---

Filter DT columns

Description

Filter a data.frame based on the DT datatable widget column search string.

Usage

filterDTColumn(x, search)

filterDT(df, column, global)

Arguments

x	A numeric or character vector, usually representing a column of a data.frame.
search	A string specifying the search filter to apply to x.
df	A data.frame that was used in the datatable widget.
column	A character vector of per-column search strings to apply to df. If any entry is an empty string, the corresponding column is not used for any filtering.
global	String containing a regular expression to search for across all columns in df (and row names, if present). If an empty string, no filtering is performed.

Details

For character x, search is treated as a regular expression.

For numeric x, search should have the form LOWER ... UPPER where all elements in [LOWER, UPPER] are retained.

For factor x, search should have the form ["choice_1", "choice_2", etc.]. This is also the case for logical x, albeit with the only choices being "true" or "false".

filterDT will retain all rows where (i) any value in any column (after coercion to a string) matches global, and (ii) the value in each column satisfies the filter specified in the corresponding entry of column. Setting global to an empty string will skip requirement (i) while setting any entry of column to an empty string will skip requirement (ii) for the affected column.

Ideally, ncol(df) and length(searches) would be the same, but if not, filterDT will simply filter on the first N entries where N is the smaller of the two.

Any NA element in x will be treated as a no-match. The same applies for each column of df that has non-empty column. Note that a no-match in one column does not preclude a successful match in another column by global.

Value

A logical vector indicating which entries of x or rows of df are to be retained.

Author(s)

Aaron Lun

See Also

datatable and associated documentation for more details about column searches.

Examples

# Regular expression:
filterDTColumn(LETTERS, "A|B|C")

# Range query:
filterDTColumn(runif(20), "0.1 ... 0.5")

# Factor query:
filterDTColumn(factor(letters), "['a', 'b', 'c']")

# Works on DataFrames:
X <- data.frame(row.names=LETTERS, thing=runif(26), 
    stuff=sample(letters[1:3], 26, replace=TRUE),
    stringsAsFactors=FALSE)

filterDT(X, c("0 ... 0.5", "a|b"), global="")
filterDT(X, "", global="A")

---

Hidden interface elements

Description

Returns an interface element with or without the CSS class shinyjs-hide, depending on whether the element is hidden based on .hideInterface. This allows panels to hide interface elements that are provided by parent classes but are not needed in the subclass.

Usage

.selectInputHidden(x, field, ...)

Arguments

x	An instance of a Panel class.
field	String specifying the name of the suffix of the ID of the interface element.
...	Further arguments to pass to the Shiny function responsible for producing the interface element.

Details

.selectInputHidden(x, field, ...) produces a Shiny selectInput element that will be hidden if .hideInterface(x) is TRUE.

Value

The output of FUN(id, ..) is returned where id is defined by concatenating .getEncodedName(x) and field (separated by an underscore).

Author(s)

Kevin Rue-Albrecht

Examples

.selectInputHidden(ComplexHeatmapPlot(), "SelectionHistory",
  choices = c(1, 2, 3), label = "Saved selection (hidden)")
  
.selectInputHidden(ReducedDimensionPlot(), "Type",
  choices = c("UMAP", "PCA"), label = "Reduced dimension type (hidden)")

---

Generics for the panel interface

Description

An overview of the generics for defining the user interface (UI) for each panel as well as some recommendations on their implementation.

Defining the parameter interface

.defineInterface(x, se, select_info) defines the UI for modifying all parameters for a given panel. The required arguments are:

• x, an instance of a Panel class.

• se, a SummarizedExperiment object containing the current dataset. This can be assumed to have been produced by running .refineParameters(x, se).

• select_info, a list of two lists, single and multiple, each of which contains the character vectors row and column. This specifies the panels available for transmitting single/multiple selections on the rows/columns, see ?.multiSelectionDimension and ?.singleSelectionDimension for more details.

Methods for this generic are expected to return a list of collapseBox elements. Each parameter box can contain arbitrary numbers of additional UI elements, each of which is expected to modify one slot of x upon user interaction.

The ID of each interface element should follow the form of PANEL_SLOT where PANEL is the panel name (from .getEncodedName(x)) and SLOT is the name of the slot modified by the interface element, e.g., "ReducedDimensionPlot1_Type". Each interface element should have an equivalent observer in .createObservers unless they are hidden by .hideInterface (see below).

It is the developer's responsibility to call callNextMethod to obtain interface elements for parent classes. A common strategy is to combine the output of callNextMethod with additional collapseBox elements to achieve the desired UI structure.

Defining the data parameter interface

.defineDataInterface(x, se, select_info) defines the UI for data-related (i.e., non-aesthetic) parameters. The required arguments are the same as those for .defineInterface. Methods for this generic are expected to return a list of UI elements for altering data-related parameters, which are automatically placed inside the “Data parameters” collapsible box. Each element's ID should still follow the PANEL_SLOT pattern described above.

This generic aims to provide a simpler alternative to specializing .defineInterface for the most common use case. New panels can write methods for this generic to add their own interface elements for altering the contents of the panel, without needing to reimplement other UI elements in the parent class's .defineInterface method. Conversely, there is no obligation to write a method for this generic if one is planning to specialize .defineInterface.

It is the developer's responsibility to call callNextMethod to obtain interface elements for parent classes.

Hiding interface elements

.hideInterface(x, field) determines whether certain UI elements should be hidden from the user. The required arguments are:

• x, an instance of a Panel class.

• field, string containing the name of a slot of x.

Methods for this generic are expected to return a logical scalar indicating whether the interface element corresponding to field should be hidden from the user. This is useful for hiding UI elements that cannot be changed or have no effect, especially in highly specialized subclasses where some concepts in the parent class may no longer be relevant. (The alternative would be to reimplement all of the parent's .defineInterface method just to omit a handful of UI elements!)

It is the developer's responsibility to call callNextMethod to hide the same interface elements as parent classes. This is not strictly required if one wishes to expose previously hidden elements.

Author(s)

Aaron Lun

---

iSEE UI element wrappers

Description

Wrapper functions to create the standard shiny user interface elements, accompanied by an optional help icon that opens an interactive tour describing the purpose of the element. Also responds to requests to hide a particular element via .hideInterface.

Usage

.selectInput.iSEE(x, field, label, ..., help = TRUE)

.selectizeInput.iSEE(x, field, label, ..., help = TRUE)

.checkboxInput.iSEE(x, field, label, ..., help = TRUE)

.checkboxGroupInput.iSEE(x, field, label, ..., help = TRUE)

.sliderInput.iSEE(x, field, label, ..., help = TRUE)

.numericInput.iSEE(x, field, label, ..., help = TRUE)

.radioButtons.iSEE(x, field, label, ..., help = TRUE)

Arguments

x	A Panel object for which to construct an interface element.
field	String containing the name of the parameter controlled by the interface element.
label	String specifying the label to be shown.
...	Further arguments to be passed to the corresponding shiny function.
help	Logical scalar indicating whether a help icon should be added to the label.

Value

The output of FUN(id, ..) is returned where FUN is set the corresponding shiny function, e.g., selectInput for .selectInput.iSEE. id is defined by concatenating .getEncodedName(x) and field (separated by an underscore).

If .hideInterface(x, field) is TRUE, the output is wrapped inside a hidden call.

Author(s)

Aaron Lun

---

iSEE: interactive SummarizedExperiment Explorer

Description

Interactive and reproducible visualization of data contained in a SummarizedExperiment object, using a Shiny interface.

Usage

iSEE(
  se,
  initial = NULL,
  extra = NULL,
  colormap = ExperimentColorMap(),
  landingPage = createLandingPage(),
  tour = NULL,
  appTitle = NULL,
  runLocal = TRUE,
  voice = FALSE,
  bugs = FALSE,
  saveState = NULL,
  ...
)

Arguments

se	A SummarizedExperiment object, ideally with named assays. If missing, an app is launched with a landing page generated by the landingPage argument.
initial	A list of Panel objects specifying the initial state of the app. The order of panels determines the sequence in which they are laid out in the interface. Defaults to one instance of each panel class available from iSEE.
extra	A list of additional Panel objects that might be added after the app has started. Defaults to one instance of each panel class available from iSEE.
colormap	An ExperimentColorMap object that defines custom colormaps to apply to individual assays, colData and rowData covariates.
landingPage	A function that renders a landing page when iSEE is started without any specified se. Ignored if se is supplied.
tour	A data.frame with the content of the interactive tour to be displayed after starting up the app. Ignored if se is not supplied.
appTitle	A string indicating the title to be displayed in the app. If not provided, the app displays the version info of iSEE.
runLocal	A logical indicating whether the app is to be run locally or remotely on a server, which determines how documentation will be accessed.
voice	A logical indicating whether the voice recognition should be enabled.
bugs	Set to TRUE to enable the bugs Easter egg. Alternatively, a named numeric vector control the respective number of each bug type (e.g., c(bugs=3L, spiders=1L)).
saveState	A function that accepts a single argument containing the current application state and saves it to some appropriate location.
...	Further arguments to pass to shinyApp.

Details

Configuring the initial state of the app is as easy as passing a list of Panel objects to initial. Each element represents one panel and is typically constructed with a command like ReducedDimensionPlot(). Panels are filled from left to right in a row-wise manner depending on the available width. Each panel can be easily customized by modifying the parameters in each object.

The extra argument should specify Panel classes that might not be shown during initialization but can be added interactively by the user after the app has started. The first instance of each new class in extra will be used as a template when the user adds a new panel of that class. Note that initial will automatically be appended to extra to form the final set of available panels, so it is not strictly necessary to re-specify instances of those initial panels in extra. (unless we want the parameters of newly created panels to be different from those at initialization).

Value

A Shiny app object is returned for interactive data exploration of se, either by simply printing the object or by explicitly running it with runApp.

Setting up a tour

The tour argument allows users to specify a custom tour to walk their audience through various panels. This is useful for describing different aspects of the dataset and highlighting interesting points in an interactive manner.

We use the format expected by the rintrojs package - see https://github.com/carlganz/rintrojs#usage for more information. There should be two columns, element and intro, with the former describing the element to highlight and the latter providing some descriptive text. The defaultTour also provides the default tour that is used in the Examples below.

Creating a landing page

If se is not supplied, a landing page is generated that allows users to upload their own RDS file to initialize the app. By default, the maximum request size for file uploads defaults to 5MB (https://shiny.rstudio.com/reference/shiny/0.14/shiny-options.html). To raise the limit (e.g., 50MB), run options(shiny.maxRequestSize=50*1024^2).

The landingPage argument can be used to alter the landing page, see createLandingPage for more details. This is useful for creating front-ends that can retrieve SummarizedExperiments from a database on demand for interactive visualization.

Saving application state

If users want to record the application state, they can download an RDS file containing a list with the entries:

• memory, a list of Panel objects containing the current state of the application. This can be directly re-used as the initial argument in a subsequent iSEE call.

• se, the SummarizedExperiment object of interest. This is optional and may not be present in the list, depending on the user specifications.

• colormap, the ExperimentColorMap object being used. This is optional and may not be present in the list, depending on the user specifications.

We can also provide a custom function in saveState that accepts a single argument containing this list. This is most useful when iSEE is deployed in an enterprise environment where sessions can be saved in a persistent location; combined with a suitable landingPage specification, this allows users to easily reload sessions of interest. The idea is very similar to Shiny bookmarks but is more customizable and can be used in conjunction with URL-based bookmarking.

References

Rue-Albrecht K, Marini F, Soneson C, Lun ATL. iSEE: Interactive SummarizedExperiment Explorer F1000Research 7.

Javascript code for bugs was based on https://github.com/Auz/Bug.

Examples

library(scRNAseq)

# Example data ----
sce <- ReprocessedAllenData(assays="tophat_counts")
class(sce)

library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")

sce <- runPCA(sce, ncomponents=4)
sce <- runTSNE(sce)
rowData(sce)$ave_count <- rowMeans(assay(sce, "tophat_counts"))
rowData(sce)$n_cells <- rowSums(assay(sce, "tophat_counts") > 0)
sce

# launch the app itself ----

app <- iSEE(sce)
if (interactive()) {
  shiny::runApp(app, port=1234)
}

---

iSEE: interactive SummarizedExperiment/SingleCellExperiment Explorer

Description

iSEE is a Bioconductor package that provides an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results, e.g., from principal components analysis (PCA) or t-distributed stochastic neighbour embedding (t-SNE)

Author(s)

Aaron Lun [email protected]

Charlotte Soneson [email protected]

Federico Marini [email protected]

Kevin Rue-Albrecht [email protected]

See Also

Useful links:

• https://github.com/iSEE/iSEE

• Report bugs at https://github.com/iSEE/iSEE/issues

---

Global iSEE options

Description

Get or set global values that are used by relevant panels during construction and application initialization. This has been deprecated in favor of panelDefaults (for options that apply during Panel construction) and registerAppOptions (for options that apply during application runtime).

Usage

iSEEOptions

Format

An object of class list of length 4.

Commands

str(iSEEOptions$get()) will show the default values for all options.

iSEEOptions$set(name=value) will set the named option to value.

iSEEOptions$restore() will reset the global options to the package default values.

Available options

point.color

Default color of data points in DotPlot panels (character).

point.size

Default size of data points in DotPlot panels (numeric).

point.alpha

Default alpha level controlling transparency of data points in DotPlot panels (numeric).

downsample

Enable visual downsampling in DotPlot panels (logical).

downsample.resolution

Resolution of the visual downsampling, if active (numeric).

selected.color

Color of selected data points in DotPlot panels (character).

selected.alpha

Alpha level controlling transparency of data points not selected in DotPlot panels (numeric).

selection.dynamic.single

Toggle dynamic single selections for all panels (logical).

selection.dynamic.multiple

Toggle dynamic multiple selections for all panels (logical).

contour.color

Color of the 2d density estimation contour in DotPlot panels (character).

font.size

Global multiplier controlling the magnification of plot title and text elements in DotPlot panels (numeric).

legend.position

Position of the legend in DotPlot and ComplexHeatmapPlot panels (one of "Bottom", "Right").

legend.direction

Position of the legend in DotPlot and ComplexHeatmapPlot panels (one of "Horizontal", "Vertical").

panel.width

Default panel grid width (must be between 1 and 12).

panel.height

Default panel height (in pixels).

panel.color

Named character vector of colors. The names of the vector should be set to the name of class to be overridden; if a class is not named here, its default color is used. It is highly recommended to define colors as hex color codes (e.g., "#1e90ff"), for full compatibility with both HTML elements and R plots.

color.maxlevels

Maximum number of levels for a categorical variable used for coloring. Variables with more levels are coerced to numeric to avoid problems with an overly-large legend. Defaults to 24.

factor.maxlevels

Maximum number of levels for a categorical variable to be used anywhere in the app. Variables with more levels are coerced to numeric to avoid rendering delays. Defaults to 100.

assay

Character vector of assay names to use if available, in order of preference.

RowTable.select.details

A function that takes a string containing the name of a feature (i.e., the current selection in the RowTable) and returns a HTML element with more details.

ColumnTable.select.details

A function that takes a string containing the name of a sample (i.e., the current selection in the ColumnTable) and returns a HTML element with more details.

Author(s)

Kevin Rue-Albrecht

Examples

iSEEOptions$get('downsample'); iSEEOptions$get('selected.color')

---

Jitter points for categorical variables

Description

Add quasi-random jitter on the x-axis for violin plots when the x-axis variable is categorical. Add random jitter within a rectangular area for square plots when both x- and y-axis variables are categorical.

Usage

jitterSquarePoints(X, Y, grouping = NULL)

jitterViolinPoints(X, Y, grouping = NULL, ...)

Arguments

X	A factor corresponding to a categorical variable.
Y	A numeric vector of the same length as X for jitterViolinPoints, or a factor of the same length as X for jitterSquarePoints.
grouping	A named list of factors of the same length as X, specifying how elements should be grouped.
...	Further arguments to be passed to offsetX.

Details

The jitterViolinPoints function calls offsetX to obtain quasi-random jittered x-axis values. This reflects the area occupied by a violin plot, though some tuning of arguments in ... may be required to get an exact match.

The jitterSquarePoints function will uniformly jitter points on both the x- and y-axes. The jitter area is a square with area proportional to the frequency of the paired levels in X and Y. If either factor only has one level, the jitter area becomes a rectangle that can be interpreted as a bar plot.

If grouping is specified, the values corresponding to each point defines a single combination of levels. Both functions will then perform jittering separately within each unique combination of levels. This is useful for obtaining appropriate jittering when points are split by group, e.g., during faceting.

If grouping!=NULL for jitterSquarePoints the statistics in the returned summary data.frame will be stratified by unique combinations of levels. To avoid clashes with existing fields, the names in grouping should not be "X", "Y", "Freq", "XWidth" or "YWidth".

Value

For jitterViolinPoints, a numeric vector is returned containing the jittered x-axis coordinates for all points.

For jitterSquarePoints, a list is returned with numeric vectors X and Y, containing jittered coordinates on the x- and y-axes respectively for all points; and summary, a data.frame of frequencies and side lengths for each unique pairing of X/Y levels.

Author(s)

Aaron Lun

Examples

X <- factor(sample(LETTERS[1:4], 100, replace=TRUE))
Y <- rnorm(100)
(out1 <- jitterViolinPoints(X=X, Y=Y))

Y2 <- factor(sample(letters[1:3], 100, replace=TRUE))
(out2 <- jitterSquarePoints(X=X, Y=Y2))

grouped <- sample(5, 100, replace=TRUE)
(out3 <- jitterViolinPoints(X=X, Y=Y, grouping=list(FacetRow=grouped)))
(out4 <- jitterSquarePoints(X=X, Y=Y2, grouping=list(FacetRow=grouped)))

---

Find rows of data within a closed lasso

Description

Identify the rows of a data.frame lying within a closed lasso polygon, analogous to brushedPoints.

Usage

lassoPoints(df, lasso)

Arguments

df	A data.frame from which to select rows.
lasso	A list containing data from a lasso.

Details

This function uses in.out from the mgcv package to identify points within a polygon. This involves a boundary crossing algorithm that may not be robust in the presence of complex polygons with intersecting edges.

Value

A subset of rows from df with coordinates lying within lasso.

Author(s)

Aaron Lun

See Also

brushedPoints

Examples

lasso <- list(coord=rbind(c(0, 0), c(0.5, 0), c(0, 0.5), c(0, 0)),
    closed=TRUE, mapping=list(x="X", y="Y"))
values <- data.frame(X=runif(100), Y=runif(100),
    row.names=sprintf("VALUE_%i", seq_len(100)))
lassoPoints(values, lasso)

# With faceting information:
lasso <- list(coord=rbind(c(0, 0), c(0.5, 0), c(0, 0.5), c(0, 0)),
    panelvar1="A", panelvar2="B", closed=TRUE,
    mapping=list(x="X", y="Y",
    panelvar1="FacetRow", panelvar2="FacetColumn"))
values <- data.frame(X=runif(100), Y=runif(100),
    FacetRow=sample(LETTERS[1:2], 100, replace=TRUE),
    FacetColumn=sample(LETTERS[1:4], 100, replace=TRUE),
    row.names=sprintf("VALUE_%i", seq_len(100)))
lassoPoints(values, lasso)

---

Manage commands to be evaluated

Description

Functions to manage commands to be evaluated.

Usage

.textEval(cmd, envir)

Arguments

cmd	A character vector containing commands to be executed.
envir	An environment in which to execute the commands.

Value

.textEval returns the output of eval(parse(text=cmd), envir), unless cmd is empty in which case it returns NULL.

Author(s)

Aaron Lun, Kevin Rue-Albrecht

Examples

myenv <- new.env()
myenv$x <- "Hello world!"
.textEval("print(x)", myenv)

---

Generics for row/column metadata plots

Description

These generics allow subclasses to refine the choices of allowable variables on the x- and y-axes of a ColumnDataPlot or RowDataPlot. This is most useful for restricting the visualization to a subset of variables, e.g., only taking log-fold changes in a y-axis of a MA plot.

Allowable y-axis choices

.allowableYAxisChoices(x, se) takes x, a Panel instance; and se, the SummarizedExperiment object. It is expected to return a character vector containing the names of acceptable variables to show on the y-axis. For ColumnDataPlots, these should be a subset of the variables in colData(se), while for RowDataPlots, these should be a subset of the variables in rowData(se).

Given a constant se, the output of this function should be constant for all instances of the same panel class. As such, it is a good idea to make use of information precomputed by .cacheCommonInfo. For example, .cacheCommonInfo,ColumnDotPlot-method will add vectors specifying whether a variable in the colData is valid and discrete or continuous, which can be intersected with any additional requirements in a subclass's method for this generic.

This generic is called by .defineDataInterface for ColumnDataPlots and RowDataPlots. Thus, developers wanting to restrict those choices for subclasses can simply specialize .allowableYAxisChoices rather than reimplementing .defineDataInterface.

Allowable x-axis choices

.allowableXAxisChoices(x, se) is the same as above but controls the variables that can be shown on the x-axis. This need not return the same subset of variables as .allowableYAxisChoices. However, again, the output of this function should be constant for all instances of the same class and a constant se.

Author(s)

Aaron Lun

---

Generics for controlling multiple selections

Description

A panel can create a multiple selection on either the rows or columns and transmit this selection to another panel to affect its set of displayed points. For example, users can brush on a DotPlots to select a set of points, and then the panel can transmit the identities of those points to another panel for highlighting.

This suite of generics controls the behavior of these multiple selections. In all of the code chunks shown below, x is assumed to be an instance of the Panel class.

Possibility of selection

.isBrushable(x) should return a logical specifying whether the panel supports selection using a Shiny brush or lasso waypoints. The output should be constant for all instances of x and is used to govern the reporting of multiple selections in the code tracker.

Specifying the dimension

.multiSelectionDimension(x) should return a string specifying whether the selection contains rows ("row"), columns ("column") or if the Panel in x does not perform multiple selections at all ("none"). The output should be constant for all instances of x and is used to govern the interface choices for the selection parameters.

Specifying the active selection

.multiSelectionActive(x) should return some structure containing all parameters required to identify all points in the active multiple selection of x. For example, the DotPlot method for this generic would return the contents of the BrushData slot, usually a list containing a Shiny brush or lasso waypoints for DotPlot classes. If .multiSelectionActive(x) returns NULL, x is assumed to have no active multiple selection.

The active selection is considered to be the one that can be directly changed by the user, as compared to saved selections that are not modifiable (other than being deleted on a first-in-last-out basis). This generic is primarily used to bundle up selection parameters to be stored in the SelectionHistory slot when the user saves the current active selection.

Evaluating the selection

.multiSelectionCommands(x, index) is expected to return a character vector of commands to generate a character vector of row or column names in the desired multiple selection of x. If index=NA, the desired selection is the currently active one; developers can assume that .multiSelectionActive(x) returns a non-NULL value in this case. Otherwise, for an integer index, it refers to the corresponding saved selection in the SelectionHistory.

The commands will be evaluated in an environment containing:

• select, a variable of the same type as returned by .multiSelectionActive(x). This will contain the active selection if index=NA and one of the saved selections otherwise. For example, for DotPlots, select will be either a Shiny brush or a lasso structure.

• contents, some arbitrary content saved by the rendering expression in .renderOutput(x). This is most often a data.frame but can be anything as long as .multiSelectionCommands knows how to process it. For example, a data.frame of coordinates is stored by DotPlots to identify the points selected by a brush/lasso.

• se, the SummarizedExperiment object containing the current dataset.

The output commands are expected to produce a character vector named selected in the evaluation environment. All other variables generated by the commands should be prefixed with . to avoid name clashes.

Determining the available points for selection

.multiSelectionAvailable(x, contents) is expected to return an integer scalar specifying the number of points available for selection in the the current instance of the panel x. The contents field in the output of .generateOutput is passed to the contents argument of this generic.

The default method for this generic returns nrow(contents) for all Panel subclasses, assuming that contents is a data.frame where each row represents a point. If not, this method needs to be specialized in order to return an accurate total of available points, which is ultimately used to compute the percentage selected in the multiple selection information panels.

Destroying selections

.multiSelectionClear(x) should return x after removing the active selection, i.e., so that nothing is selected. This is used internally to remove multiple selections that do not make sense after protected parameters have changed. For example, a brush or lasso made on a PCA plot in ReducedDimensionPlots would not make sense after switching to t-SNE coordinates, so the application will automatically erase those selections to avoid misleading conclusions.

Responding to selections

These generics control how x responds to a transmitted multiple selection, not how x itself transmits selections.

.multiSelectionRestricted(x) should return a logical scalar indicating whether x's displayed contents will be restricted to the selection transmitted from another panel. This is used to determine whether child panels of x need to be re-rendered when x's transmitter changes its multiple selection. For example, the method for RowDotPlots and ColumnDotPlots would return TRUE if RowSelectionRestrict=TRUE or ColumnSelectionRestrict=TRUE, respectively. Otherwise, it would be FALSE as the transmitted selection is only used for aesthetics, not for changing the identity of the displayed points.

.multiSelectionInvalidated(x) should return a logical scalar indicating whether a transmission of a multiple selection to x invalidates x's own existing selections. This should only be TRUE in special circumstances, e.g., if receipt of a new multiple selection causes recalculation of coordinates in a DotPlot.

.multiSelectionResponsive(x, dims) should return a logical scalar indicating whether x is responsive to an incoming multiple selection on dimensions dims. For example, the method for ComplexHeatmapPlot would return TRUE when an incoming selection originates from a row-oriented panel and CustomRows=FALSE. Otherwise, it would be FALSE as the dimension of the transmitted selection is dismissed by the options of the child panel.

Author(s)

Aaron Lun

---

Convert multiple selections into a factor

Description

Convert multiple selection information into a factor, typically for use as a covariate or for coloring.

Usage

multiSelectionToFactor(selected, all.names)

Arguments

selected	A named list of character vectors, containing the names of selected observations for different selections. Vectors for different selections may overlap.
all.names	Character vector of all observations.

Value

A factor containing the set(s) to which each observation is assigned. Multiple sets are encoded as comma-separated strings. Unselected observations are listed as "unselected".

Author(s)

Aaron Lun

Examples

multiSelectionToFactor(list(active=c("A", "B"), 
    saved1=c("B", "C"), saved2=c("D", "E", "F")),
    all.names=LETTERS[1:10])

---

Generic for the panel observers

Description

The workhorse generic for defining the Shiny observers for a given panel, along with recommendations on its implementation.

Creating parameter observers

In .createObservers(x, se, input, session, pObjects, rObjects), the required arguments are:

• x, an instance of a Panel class.

• se, a SummarizedExperiment object containing the current dataset. This can be assumed to have been produced by running .refineParameters(x, se).

• input, the Shiny input object from the server function.

• session, the Shiny session object from the server function.

• pObjects, an environment containing global parameters generated in the iSEE app.

• rObjects, a reactive list of values generated in the iSEE app.

Methods for this generic are expected to set up all observers required to respond to changes in the interface elements set up by .defineInterface. Recall that each interface element has an ID of the form of PANEL_SLOT, where PANEL is the panel name (from .getEncodedName) and SLOT is the name of the slot modified by the interface element. Thus, observers should respond to changes in those elements in input. The return value of this generic is not used; only the side-effect of observer set-up is relevant.

It is the developer's responsibility to call callNextMethod to set up the observers required by the parent class. This is best done by calling callNextMethod at the top of the method before defining up additional observers. Each parent class should implement observers for its slots, so it is usually only necessary to implement observers for any newly added slots in a particular class.

Modifying the memory

Consider an observer for an interface element that modifies a slot of x. The code within this observer is expected to modify the “memory” of the app state in pObjects, via:

new_value <- input[[paste0(PANEL, "_", SLOT)]]
pObjects$memory[[PANEL]][[SLOT]] <- new_value

This enables iSEE to keep a record of the current state of the application. In fact, any changes must go through pObjects$memory before they change the output in .renderOutput; there is no direct interaction between input and output in this framework.

We suggest using .createProtectedParameterObservers and .createUnprotectedParameterObservers, which create simple observers that update the memory in response to changes in the UI elements. For handling selectize elements filled with server-side row/column names, we can use .createCustomDimnamesModalObservers.

Developers should not attempt to modify x in any observer expression. This value does not have pass-by-reference semantics and any changes will not propagate to other parts of the application. Rather, modifications should occur to the version of x in pObjects$memory, as described in the code chunk above.

Triggering re-rendering

To trigger re-rendering of an output, observers should call .requestUpdate(PANEL, rObjects) where PANEL is the name of the current panel This will request a re-rendering of the output with no additional side effects and is most useful for responding to aesthetic parameters.

In some cases, changes to some parameters may invalidate existing multiple selections, e.g., brushes and lassos are no longer valid if the variable on the axes are altered. Observers responding to such changes should instead call .requestCleanUpdate(PANEL, pObjects, rObjects), which will destroy all existing selections in order to avoid misleading conclusions.

Author(s)

Aaron Lun

---

Generics for Panel outputs

Description

An overview of the generics for defining the panel outputs, along with recommendations on their implementation.

Defining the output element

.defineOutput(x) defines the output element of the panel (e.g., a plot or table widget), given an instance of a Panel subclass in x.

Methods for this generic are expected to return a HTML element containing the visual output of the panel, such as the return value of plotOutput or dataTableOutput. This element will be shown in the iSEE interface above the parameter boxes for x. Multiple elements can be returned via a tagList.

The IDs of the output elements are expected to be prefixed with the panel name from .getEncodedName(x) and an underscore, e.g., "ReducedDimensionPlot1_someOutput". One of the output elements may simply have the ID set to PANEL alone; this is usually the case for simple panels with one primary output like a DotPlot.

Defining the rendered output

.renderOutput(x, se, ..., output, pObjects, rObjects) will create an expression to render the panel's output. The following arguments are required:

• x, an instance of a Panel class.

• se, a SummarizedExperiment object containing the current dataset.

• ..., further arguments that may be used by specific methods.

• output, the Shiny output object from the server function.

• pObjects, an environment containing global parameters generated in the iSEE app.

• rObjects, a reactive list of values generated in the iSEE app.

It is expected to attach one or more reactive expressions to output to render the output element(s) defined by .defineOutput. This is typically done by calling shiny rendering functions like renderPlot or the most appropriate equivalent for the panel's output. The return value of this generic is not used; only the side-effect of the reactive output set-up is relevant.

The rendering expression inside the chosen rendering function is expected to:

1. Call force(rObjects[[PANEL]]), where PANEL is the output of .getEncodedName(x). This ensures that the output is rerendered upon requesting changes in .requestUpdate.

2. Call .generateOutput to generate the output content to be rendered.

3. Fill pObjects$contents[[PANEL]] with some content related to the displayed output that allows cross-referencing with single/multiple selection structures. This will be used in other generics like .multiSelectionCommands and .singleSelectionValue to determine the identity of the selected point(s). As a result, it is only strictly necessary if the panel is a potential transmitter, as determined by the return value of .multiSelectionDimension.

4. Fill pObjects$commands[[PANEL]] with a character vector of commands required to produce the displayed output. This should minimally include the commands required to generate pObjects$contents[[PANEL]]; for plotting panels, the vector should also include code to create the plot.

5. Fill pObjects$varname[[PANEL]] with a string containing the R expression in pObjects$commands[[PANEL]] that holds the contents stored in pObjects$contents[[PANEL]]. This is used for code reporting, and again, is only strictly necessary if the panel is a potential transmitter.

We strongly recommend calling .retrieveOutput within the rendering expression, which will automatically perform all of the tasks above, rather than calling .generateOutput manually. By doing so, the only extra work required of the rendering expression is to actually render the output (e.g., by printing a ggplot object). Of course, the rendering expression must itself be encapsulated by an appropriate rendering function assigned to output.

Developers should not attempt to modify x in any rendering expression. This does not have pass-by-reference semantics and any changes will not propagate to other parts of the application. Similarly, the rendering expression should treat pObjects$memory as read-only. Any adjustment of parameters should be handled elsewhere, e.g., by the observer expressions in .createObservers.

Generating content

.generateOutput(x, se, all_memory, all_contents) actually generates the panel's output to be used in the rendering expression. The following arguments are required:

• x, an instance of a Panel class.

• se, a SummarizedExperiment object containing the current dataset.

• all_memory, a named list containing Panel objects parameterizing the current state of the app.

• all_contents, a named list containing the contents of each panel.

Methods for this generic should return a list containing:

• contents, some arbitrary content for the panel (usually a data.frame). The values therein are used by .multiSelectionCommands to determine the multiple row/column selection in x to be transmitted to other (child) panels. The app will ensure that the pObjects$contents of each panel is populated before attempting to render their children. contents may be set to NULL if x does not transmit, i.e., .multiSelectionDimension returns "none".

• commands, a list of character vectors of R commands that, when executed, produces the contents of the panel and any displayed output (e.g., a ggplot object). Developers should write these commands as if the evaluation environment only contains the SummarizedExperiment se and ExperimentColorMap colormap. It may also contain col_selected, if a multiple column selection is being transmitted to x; and possibly row_selected, if a multiple row selection is being transmitted to x.

• varname, a string specifying the name of the variable in commands used to generate contents. This is used to fulfill code tracking obligations. If the current panel is not a transmitter, this may be set to NULL instead.

The output list may contain any number of other fields that can be used by .renderOutput but are otherwise ignored.

We suggest implementing this method using eval(parse(text=...)) calls, which enables easy construction and evaluation of the commands and contents at the same time. A convenient wrapper for this call is provided by the .textEval utility.

The all_memory and all_contents arguments are provided for the sole purpose of determining what multiple selections are being received by x. We strongly recommend passing them onto .processMultiSelections to do the heavy lifting. It would be unusual and inadvisable to use these arguments for any other information sharing across panels.

Exporting content

.exportOutput(x, se, all_memory, all_contents) converts the panel output into a downloadable form. The following arguments are required:

• x, an instance of a Panel class.

• se, a SummarizedExperiment object containing the current dataset.

• all_memory, a named list containing Panel objects parameterizing the current state of the app.

• all_contents, a named list containing the contents of each panel.

Methods for this generic should generate appropriate files containing the content of x. (For example, plots may create PDFs while tables may create CSV files.) All files should be created in the working directory at the time of the function call, possibly in further subdirectories. Each file name should be prefixed with the .getEncodedName. The method itself should return a character vector containing relative paths to all newly created files.

To implement this method, we suggest simply passing all arguments onto .generateOutput and then converting the output into an appropriate file.

Author(s)

Aaron Lun

---

The Panel virtual class

Description

The Panel is a virtual base class for all iSEE panels. It provides slots and methods to control the height and width of each panel, as well as functionality to control the choice of “transmitting” panels from which to receive a multiple row/column selection.

Slot overview

The following slots are relevant to panel organization:

• PanelId, an integer scalar specifying the identifier for the panel. This should be unique across panels of the same concrete class.

• PanelWidth, an integer scalar specifying the width of the panel. Bootstrap coordinates are used so this value should lie between 2 and 12; defaults to 4 in getPanelDefault.

• PanelHeight, an integer scalar specifying the height of the panel in pixels. This is expected to lie between 400 and 1000; defaults to 500 in getPanelDefault.

The following slots are relevant to receiving a multiple selection on the rows:

• RowSelectionSource, a string specifying the name of the transmitting panel from which to receive a multiple row selection (e.g., "RowDataPlot1"). Defaults to "---".

• RowSelectionDynamicSource, a logical scalar indicating whether x should dynamically change its selection source for multiple row selections. Defaults to FALSE in getPanelDefault.

• RowSelectionRestrict, a logical scalar indicating whether the display of x should be restricted to the rows in the multiple selection received from a transmitting panel. Defaults to FALSE.

The following slots are relevant to receiving a multiple selection on the columns:

• ColumnSelectionSource, a string specifying the name of the transmitting panel from which to receive a multiple column selection (e.g., "ColumnDataPlot1"). Defaults to "---".

• ColumnSelectionDynamicSource, a logical scalar indicating whether x should dynamically change its selection source for multiple column selections. Defaults to FALSE in getPanelDefault.

• ColumnSelectionRestrict, a logical scalar indicating whether the display of x should be restricted to the columns in the multiple selection received from a transmitting panel. Defaults to FALSE.

There are also the following miscellaneous slots:

• SelectionBoxOpen, a logical scalar indicating whether the selection parameter box should be open at initialization. Defaults to FALSE.

• SelectionHistory, a list of arbitrary elements that contain parameters for saved multiple selections. Each element of this list corresponds to one saved selection in the current panel. Defaults to an empty list.

• VersionInfo, a named list of package_version objects specifying the versions of packages used to create a given Panel instance. This information is used to inform updateObject of any updates that need to be applied. By default, it is filled with a single "iSEE" entry containing the current version of iSEE.

Getting and setting slots

In all of the following code chunks, x is an instance of a Panel, and i is a string containing the slot name:

• x[[i]] returns the value of a slot named i.

• x[[i]] <- value modifies x so that the value in slot i is replaced with value.

• show(x) will print a summary of all (non-hidden) slots and their values.

Supported methods

In the following code snippets, x is an instance of a ColumnDotPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .refineParameters(x, se) calls updateObject(x). If x is up to date, this operation is a no-op and returns x without modification.

• .cacheCommonInfo(x, se) is a no-op, returning se without modification.

For defining the interface:

• .defineInterface(x, se, select_info) will return a list of collapsible boxes for changing data and selection parameters. The data parameter box will be populated based on .defineDataInterface.

• .defineDataInterface(x, se, select_info) will return an empty list.

• .hideInterface(x, field) will always return FALSE.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) will add observers to respond to changes in multiple selection options. It will also call .singleSelectionSlots(x) to set up observers for responding to transmitted single selections.

• .renderOutput(x, se, output, pObjects, rObjects) will add elements to output for rendering the information textboxes at the bottom of each panel. Each panel should specialize this method to add rendering expressions for the actual output (e.g., plots, tables), followed by a callNextMethod to create the textboxes.

For generating output:

• .exportOutput(x, se, all_memory, all_contents) is a no-op, i.e., it will return an empty character vector and create no files.

For documentation:

• .definePanelTour(x) returns a data.frame containing the selection-related steps of the tour.

For controlling selections:

• .multiSelectionRestricted(x) will always return TRUE.

• .multiSelectionDimension(x) will always return "none".

• .multiSelectionActive(x) will always return NULL.

• .multiSelectionClear(x) will always return x.

• .multiSelectionInvalidated(x) will always return FALSE.

• .multiSelectionAvailable(x, contents) will return nrow(contents).

• .singleSelectionDimension(x) will always return "none".

• .singleSelectionValue(x) will always return NULL.

• .singleSelectionSlots(x) will always return an empty list.

Subclass expectations

Subclasses are required to implement methods for:

• .defineOutput

• .generateOutput

• .renderOutput

• .fullName

• .panelColor

Subclasses that transmit selections should also implement specialized methods for selection-related parameters listed above.

Author(s)

Aaron Lun

See Also

DotPlot and Table, for examples of direct subclasses.

---

Panel defaults

Description

Get or set default parameters that are used by certain Panel during their construction. This allows users to easily change the defaults for multiple panels simultaneously without having to manually specify them in the constructor.

Usage

panelDefaults(...)

getPanelDefault(name, error = TRUE)

Arguments

...	Named options to set. Alternatively a single named list containing the options to set.
name	String containing the name of the option to retrieve. Alternatively NULL, in which case the current values of all options are returned as a named list.
error	Logical scalar indicating whether an error should be raised if name cannot be found.

Details

All options set by panelDefaults will only affect Panel construction and have no effect on the behavior of Panels that are already constructed. Most options are named after the affected slot in the relevant Panel subclass.

For general Panels:

• PanelWidth, defaults to 4.

• PanelHeight, defaults to 500.

For DotPlots:

• ColorByDefaultColor, defaults to "black".

• PointSize, defaults to 1.

• PointAlpha, defaults to 1.

• Downsample, defaults to FALSE.

• DownsampleResolution, defaults to 200.

• SelectionAlpha, defaults to 0.1.

• ContourColor, defaults to "blue".

• FontSize, defaults to 1.

• LegendPointSize, defaults to 1.

For RowDotPlots:

• TooltipRowData, defaults to character(0).

For ColumnDotPlots:

• TooltipColumnData, defaults to character(0).

For ComplexHeatmapPlots:

• LegendDirection, defaults to "Horizontal".

A few options affect multiple subclasses that independently define the same slot:

• LegendPosition, defaults to "Bottom". Affects DotPlots and ComplexHeatmapPlots.

• Assay, defaults to "logcounts". Affects FeatureAssayPlots, SampleAssayPlots and ComplexHeatmapPlots.

A few options are not named after any particular slot as they affect different slots in different subclasses:

• ColorByNameColor, defaults to "red". This affects ColorByFeatureNameColor in RowDotPlots and ColorBySampleNameColor in ColumnDotPlots.

• ColorByNameAssay, defaults to "logcounts". This affects ColorByFeatureNameAssay in RowDotPlots and ColorBySampleNameAssay in ColumnDotPlots.

• SingleSelectionDynamicSource, defaults to FALSE. This affects ColorByFeatureDynamicSource, ColorBySampleDynamicSource, XAxisFeatureDynamicSource, YAxisFeatureDynamicSource, XAxisSampleDynamicSource and YAxisSampleDynamicSource in the relevant panels.

• MultipleSelectionDynamicSource, defaults to FALSE. This affects RowSelectionDynamicSource and ColumnSelectionDynamicSource.

Value

panelDefaults will return a named list of the values of all options. If ... is non-empty, panelDefaults will modify the global options that are used during the constructors for the relevant Panel classes. (Note that the return value still contains the values before the modification is applied.)

getPanelDefault will return the current value of the requested option. If error=TRUE and name is not present, an error is raised; otherwise NULL is returned.

For developers

Developers of Panel subclasses may add more options to this list, typically by calling panelDefaults in the .onLoad expressions of the package containing the subclass. We recommend prefixing any options with the name of the package in the form of <PACKAGE>_<OPTION>, so as to avoid conflicts with other options (in the base classes, or in other downstream packages) that have the same name. Any options added in this manner should correspond to parameters that are already present as slots in the panel class. If this is not the case, consider using registerAppOptions instead.

Author(s)

Kevin Rue-Albrecht

Examples

old <- panelDefaults(Assay="WHEE")
getPanelDefault("Assay")

old <- panelDefaults(Assay="FOO", PointSize=5)
getPanelDefault("Assay")
getPanelDefault("PointSize")

# We can also list out all options:
panelDefaults()

# Restoring the previous defaults.
panelDefaults(old)
getPanelDefault("Assay")
getPanelDefault("PointSize")

---

Generics for DotPlot plotting

Description

A series of generics for controlling how plotting is performed in DotPlot panels. DotPlot subclasses can specialize one or more of them to modify the behavior of .generateOutput.

Generating plotting data

.generateDotPlotData(x, envir) sets up the data to use in the DotPlot plot. The following arguments are required:

• x, an instance of a DotPlot subclass.

• envir, the evaluation environment in which the data.frame is to be constructed. This can be assumed to have se, the SummarizedExperiment object containing the current dataset; possibly col_selected, if a multiple column selection is being transmitted to x; and possibly row_selected, if a multiple row selection is being transmitted to x.

A method for this generic should add a plot.data variable in envir containing a data.frame with columns named "X" and "Y", denoting the variables to show on the x- and y-axes respectively. It should return a list with commands, a character vector of commands that produces plot.data when evaluated in envir; and labels, a list of strings containing labels for the x-axis (named "X"), y-axis ("Y") and plot ("title").

Each row of the plot.data data.frame should correspond to one row or column in the SummarizedExperiment envir$se for RowDotPlots and ColumnDotPlots respectively. Note that, even if only a subset of rows/columns in the SummarizedExperiment are to be shown, there must always be one row in the data.frame per row/column of the SummarizedExperiment, and in the same order. All other rows of the data.frame should be filled in with NAs rather than omitted entirely. This is necessary for correct interactions with later methods that add other variables to plot.data.

Any internal variables that are generated by the commands in commands should be prefixed with . to avoid potential clashes with reserved variable names in the rest of the application.

This generic is called by .generateDotPlot (see below), which is in turn called by .generateOutput. The idea is that developers can specialize .generateDotPlotData to change the data source for a DotPlot subclass without needing to reimplement the entirety of .generateDotPlot.

Generating the ggplot object

.generateDotPlot(x, labels, envir) creates the plot to be shown in the interface. The following arguments are required:

• x, an instance of a DotPlot subclass.

• labels, a list of labels corresponding to the columns of plot.data. This is typically used to define axis or legend labels in the plot.

• envir, the evaluation environment in which the ggplot object is to be constructed. This can be assumed to have plot.data, a data.frame of plotting data.

  Note that se, row_selected and col_selected will still be present in envir, but it is simplest to only use information that has already been incorporated into plot.data where possible. This is because the order and number of rows in plot.data may have changed since .generateDotPlotData.

Methods for this generic should return a list with plot, a ggplot object; and commands, a character vector of commands to produce that object when evaluated inside envir. This plot will subsequently be the rendered output in .renderOutput. Note that envir should contain a copy of the plot object in a variable named dot.plot - see below for details.

Methods are expected to respond to the presence of various fields in the plot.data. The data.frame will contain, at the very least, the fields "X" and "Y" from .generateDotPlotData. Depending on the parameters of x, it may also have the following columns:

• "ColorBy", the values of the covariate to use to color each point.

• "ShapeBy", the values of the covariate to use for shaping each point. This is guaranteed to be categorical.

• "SizeBy", the values of the covariate to use for sizing each point. This is guaranteed to be continuous.

• "FacetRow", the values of the covariate to use to create row facets. This is guaranteed to be categorical.

• "FacetColumn", the values of the covariate to use to create column facets. This is guaranteed to be categorical.

• "SelectBy", a logical field indicating whether the point was included in a multiple selection (i.e., transmitted from another plot with x as the receiver). Note that if RowSelectionRestrict=TRUE or ColumnSelectionRestrict=TRUE (for RowDotPlots and ColumnDotPlots, respectively), plot.data will already have been subsetted to only retain TRUE values of this field.

envir may also contain the following variables:

• plot.data.all, present when a multiple selection is transmitted to x and RowSelectionRestrict=TRUE or ColumnSelectionRestrict=TRUE (for RowDotPlots and ColumnDotPlots, respectively). This is a data.frame that contains all points prior to subsetting and is useful for defining the boundaries of the plot such that they do not change when the transmitted multiple selection changes.

• plot.data.pre, present when downsampling is turned on. This is a data.frame that contains all points prior to downsampling (but after subsetting, if that was performed) and is again mainly used to fix the boundaries of the plot.

Developers may wish to use the .addMultiSelectionPlotCommands utility to draw brushes and lassos of x. Note that this refers to the brushes and lassos made on x itself, not those transmitted from another panel to x.

It would be very unwise for methods to alter the x-axis, y-axis or faceting values in plot.data. This will lead to unintuitive discrepancies between apparent visual selections for a brush/lasso and the actual multiple selection that is evaluated by downstream functions like .processMultiSelections.

In certain situations, a DotPlot subclass may be able to build off a ggplot generated by its parent class. This is easily done by exploiting the fact that methods for this generic are expected to store a copy of their plot ggplot object as a dot.plot variable in envir. A specialized method for the subclass can callNextMethod() to populate envir with the initial dot.plot, and then just construct and execute commands to add more ggplot2 layers as desired.

This generic is called by .generateOutput for DotPlot subclasses. Again, the idea here is that developers can specialize .generateDotPlot to change the plot aesthetics without needing to reimplement the entirety of .generateOutput.

Prioritizing points

.prioritizeDotPlotData(x, envir) specifies the “priority” of points to be plotted, where high-priority points are plotted last so that they will not be masked by other points. The following arguments are required:

• x, an instance of a DotPlot subclass.

• envir, the evaluation environment in which the ggplot object is to be constructed. This can be assumed to have plot.data, a data.frame of plotting data.

  Again, note that se, row_selected and col_selected will still be present in envir, but it is simplest to only use information that has already been incorporated into plot.data where possible. This is because the order and number of rows in plot.data may have changed since .generateDotPlotData.

Methods for this generic are expected to generate a .priority variable in envir, an ordered factor of length equal to nrow(plot.data) indicating the priority of each point. They may also generate a .rescaled variable, a named numeric vector containing the scaling factor to apply to the downsampling resolution for each level of .priority.

The method itself should return a list containing commands, a character vector of R commands required to generate these variables; and rescaled, a logical scalar indicating whether a .rescaled variable was produced.

Points assigned the highest level in .priority are regarded as having the highest visual importance. Such points will be shown on top of other points if there are overlaps on the plot, allowing developers to specify that, e.g., DE genes should be shown on top of non-DE genes. Scaling of the resolution enables developers to perform more aggressive downsampling for unimportant points.

Methods for this generic may also return NULL, in which case no special action is taken.

This generic is called by .generateDotPlot, which is in turn called by .generateOutput. Thus, developers of DotPlot subclasses can specialize this generic to change the point priority without needing to reimplement the entirety of .generateDotPlot.

Controlling the “None” color scale

In some cases, it is desirable to insert a default scale when ColorBy="None". This is useful for highlighting points in a manner that is integral to the nature of the plot, e.g., up- or down-regulated genes in a MA plot. We provide a few generics to help control which points are highlighted and how they are colored.

.colorByNoneDotPlotField(x) expects x, an instance of a DotPlot subclass, and returns a string containing a name of a column in plot.data to use for coloring in the ggplot mapping. This assumes that the relevant field was added to plot.data by a method for .generateDotPlotData.

.colorByNoneDotPlotScale(x) expects x, an instance of a DotPlot subclass, and returns a string containing a ggplot2 scale_color_* call, e.g., scale_color_manual. This string should end with a "+" operator as additional ggplot2 layers will be added by iSEE.

This generic is called by .generateDotPlot, which is in turn called by .generateOutput. Thus, developers of DotPlot subclasses can specialize this generic to change the default color scheme without needing to reimplement the entirety of .generateDotPlot.

Author(s)

Kevin “K-pop” Rue-Albrecht, Aaron “A-bomb” Lun

---

Process faceting choices

Description

Generate ggplot instructions to facet a plot by row and/or column

Usage

.addFacets(x)

Arguments

x	A single-row DataFrame that contains all the input settings for the current panel.

Value

A string containing a command to define the row and column faceting covariates.

Author(s)

Kevin Rue-Albrecht.

Examples

x <- ReducedDimensionPlot(
    FacetRowBy = "Column data", FacetRowByColData="Covariate_1", 
    FacetColumnBy = "Column data", FacetColumnByColData="Covariate_2") 
.addFacets(x)

---

The ReducedDimensionPlot panel

Description

The ReducedDimensionPlot is a panel class for creating a ColumnDotPlot where the coordinates of each column/sample are taken from the reducedDims of a SingleCellExperiment object. It provides slots and methods to specify which dimensionality reduction result to use and to create the data.frame with the coordinates of the specified results for plotting.

ReducedDimensionPlot slot overview

The following slots control the dimensionality reduction result that is used:

• Type, a string specifying the name of the dimensionality reduction result. If NA, defaults to the first entry of reducedDims.

• XAxis, integer scalar specifying the dimension to plot on the x-axis. Defaults to 1.

• YAxis, integer scalar specifying the dimension to plot on the y-axis. Defaults to 2.

In addition, this class inherits all slots from its parent ColumnDotPlot, DotPlot and Panel classes.

Constructor

ReducedDimensionPlot(...) creates an instance of a ReducedDimensionPlot class, where any slot and its value can be passed to ... as a named argument.

Supported methods

In the following code snippets, x is an instance of a ReducedDimensionPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .cacheCommonInfo(x) adds a "ReducedDimensionPlot" entry containing valid.reducedDim.names, a character vector of names of valid dimensionality reduction results (i.e., at least one dimension). This will also call the equivalent ColumnDotPlot method.

• .refineParameters(x, se) replaces NA values in RedDimType with the first valid dimensionality reduction result name in se. This will also call the equivalent ColumnDotPlot method for further refinements to x. If no dimensionality reduction results are available, NULL is returned instead.

For defining the interface:

• .defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.

• .panelColor(x) will return the specified default color for this panel class.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes. This will also call the equivalent ColumnDotPlot method.

For defining the panel name:

• .fullName(x) will return "Reduced dimension plot".

For creating the plot:

• .generateDotPlotData(x, envir) will create a data.frame of reduced dimension coordinates in envir. It will return the commands required to do so as well as a list of labels.

For documentation:

• .definePanelTour(x) returns an data.frame containing a panel-specific tour.

Subclasses do not have to provide any methods, as this is a concrete class.

Author(s)

Aaron Lun

See Also

ColumnDotPlot, for the immediate parent class.

Examples

#################
# For end-users #
#################

x <- ReducedDimensionPlot()
x[["Type"]]
x[["Type"]] <- "TSNE"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)

# Spits out a NULL and a warning if no reducedDims are available.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
sce <- runPCA(sce)
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

---

Set and get app-level options

Description

Set and get global options for the iSEE application. These are options that do not correspond to any Panel slot and cannot be changed by the user after initialization.

Usage

registerAppOptions(se, ...)

getAppOption(name, se, default = NULL)

getAllAppOptions(se)

Arguments

se	The SummarizedExperiment object to be supplied to iSEE.
...	Named options to register. Alternatively a single named list containing the options to register.
name	String containing the name of the option to retrieve.
default	Value to return if name is not present in the available options.

Details

registerAppOptions provides an alternative mechanism for setting global options, separate from panelDefaults. The primary difference is that registerAppOptions allows tuning of options that do not have a corresponding slot in any Panel subclass. This makes it useful for parameters that the user should not or cannot change within the application, as well as for fine-tuning parameters that are too rarely used to have their own interface elements.

Known options include:

panel.color

Named character vector of colors. The names of the vector should be set to the name of class to be overridden; if a class is not named here, its default color is used. It is highly recommended to define colors as hex color codes (e.g., "#1e90ff"), for full compatibility with both HTML elements and R plots.

color.maxlevels

Maximum number of levels for a categorical variable used for coloring. Variables with more levels are coerced to numeric to avoid problems with an overly-large legend. Defaults to 24.

factor.maxlevels

Maximum number of levels for a categorical variable to be used anywhere in the app. Variables with more levels are coerced to numeric to avoid rendering delays. Defaults to 100.

RowTable.select.details

A function that takes a string containing the name of a feature (i.e., the current selection in the RowTable) and returns a HTML element with more details.

ColumnTable.select.details

A function that takes a string containing the name of a sample (i.e., the current selection in the ColumnTable) and returns a HTML element with more details.

tooltip.signif

Number of significant digits to display in the tooltip. Defaults to 6.

The registered options are stored in the SummarizedExperiment to ensure that we can recover the application state with the combination of the SummarizedExperiment and list of Panel settings. By comparison, if we had used a global cache as in panelDefaults, we would need to save them separately to ensure that we can recover a particular application state.

By default, registerAppOptions will add or replace individual arguments specified by .... This means that users can call the function multiple times to accumulate registered options in se. The exception is if ... contains a single list, in which case the entire set of options is directly replaced by that list. For example, one could supply a single empty list to clear se of all existing options.

Value

registerAppOptions will return se, modified with the application-level options.

getAppOption will return the value of the specified option, or default if that option is not available.

getAllAppOptions will return a named list of all registered options.

For developers

Developers of Panel subclasses can add arbitrary options to ... to help control the behavior of their Panel instances. We recommend prefixing any options with the name of the package in the form of <PACKAGE>_<OPTION>, so as to avoid conflicts with other options (in the base classes, or in other downstream packages) that have the same name.

For calls to getAppOption that occur after the iSEE app has started, it is not actually necessary to supply se. The options in se are transferred to a global option store when the app starts, allowing us to call getAppOption without se in various Panel methods. This is useful for some generics where se is not part of the function signature. Developers can mimic this state (e.g., for unit testing) by calling .activateAppOptionRegistry on the SummarizedExperiment produced by registerAppOptions. Conversely, calling .deactivateAppOptionRegistry will reset the global option store.

Author(s)

Aaron Lun

Examples

se <- SummarizedExperiment()
se <- registerAppOptions(se, factor.maxlevels=10, color.maxlevels=10)

getAppOption("factor.maxlevels", se)
getAppOption("color.maxlevels", se)
getAppOption("random.other.thing", se, default=10)

getAllAppOptions(se)

# For developers: you don't actually need to pass 'se' to the getters
# if they are being called inside Panel methods.
.activateAppOptionRegistry(se)
getAppOption("factor.maxlevels")
getAppOption("color.maxlevels")
.deactivateAppOptionRegistry()

# Wiping out all options.
se <- registerAppOptions(se, list())
getAllAppOptions(se)

---

The RowDataPlot panel

Description

The RowDataPlot is a panel class for creating a RowDotPlot where the y-axis represents a variable from the rowData of a SummarizedExperiment object. It provides slots and methods for specifying which variable to use on the y-axis (and, optionally, also the x-axis), as well as a method to create the data.frame in preparation for plotting.

Slot overview

The following slots control the variables to be shown:

• YAxis, a string specifying the row of the rowData to show on the y-axis. If NA, defaults to the first valid field (see ?".refineParameters,RowDotPlot-method").

• XAxis, string specifying what should be plotting on the x-axis. This can be any one of "None", "Row data" and "Row selection". Defaults to "None".

• XAxisRowData, string specifying the row of the rowData to show on the x-axis. If NA, defaults to the first valid field.

In addition, this class inherits all slots from its parent RowDotPlot, DotPlot and Panel classes.

Constructor

RowDataPlot(...) creates an instance of a RowDataPlot class, where any slot and its value can be passed to ... as a named argument.

Supported methods

In the following code snippets, x is an instance of a RowDataPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .refineParameters(x, se) returns x after replacing any NA value in YAxis or XAxisRowData with the name of the first valid rowData variable. This will also call the equivalent RowDotPlot method for further refinements to x. If no valid row metadata variables are available, NULL is returned instead.

For defining the interface:

• .defineDataInterface(x, se, select_info) returns a list of interface elements for manipulating all slots described above.

• .panelColor(x) will return the specified default color for this panel class.

• .allowableXAxisChoices(x, se) returns a character vector specifying the acceptable variables in rowData(se) that can be used as choices for the x-axis. This consists of all variables with atomic values.

• .allowableYAxisChoices(x, se) returns a character vector specifying the acceptable variables in rowData(se) that can be used as choices for the y-axis. This consists of all variables with atomic values.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots described above and in the parent classes. This will also call the equivalent RowDotPlot method.

For controlling selections:

• .multiSelectionInvalidated(x) returns TRUE if the x-axis uses multiple row selections, such that the point coordinates may change upon updates to upstream selections in transmitting panels. Otherwise, it dispatches to the RowDotPlot method.

For defining the panel name:

• .fullName(x) will return "Row data plot".

For creating the plot:

• .generateDotPlotData(x, envir) will create a data.frame of row metadata variables in envir. It will return the commands required to do so as well as a list of labels.

For documentation:

• .definePanelTour(x) returns an data.frame containing a panel-specific tour.

Subclass expectations

Subclasses do not have to provide any methods, as this is a concrete class.

Author(s)

Aaron Lun

See Also

RowDotPlot, for the immediate parent class.

Examples

#################
# For end-users #
#################

x <- RowDataPlot()
x[["XAxis"]]
x[["XAxis"]] <- "Row data"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)

# Spits out a NULL and a warning if is nothing to plot.
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

# Replaces the default with something sensible.
rowData(sce)$Stuff <- runif(nrow(sce))
sce0 <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce0)

---

The RowDataTable panel

Description

The RowDataTable is a panel class for creating a ColumnTable where the value of the table is defined as the rowData of the SummarizedExperiment. It provides functionality to extract the rowData to coerce it into an appropriate data.frame in preparation for rendering.

Slot overview

This class inherits all slots from its parent ColumnTable and Table classes.

Constructor

RowDataTable(...) creates an instance of a RowDataTable class, where any slot and its value can be passed to ... as a named argument.

Note that ColSearch should be a character vector of length equal to the total number of columns in the rowData, though only the entries for the atomic fields will actually be used.

Supported methods

In the following code snippets, x is an instance of a RowDataTable class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .cacheCommonInfo(x) adds a "RowDataTable" entry containing valid.rowData.names, a character vector of names of atomic columns of the rowData. This will also call the equivalent ColumnTable method.

• .refineParameters(x, se) adjusts ColSearch to a character vector of length equal to the number of atomic fields in the rowData. This will also call the equivalent ColumnTable method for further refinements to x.

For defining the interface:

• .fullName(x) will return "Row data table".

• .panelColor(x) will return the specified default color for this panel class.

For creating the output:

• .generateTable(x, envir) will modify envir to contain the relevant data.frame for display, while returning a character vector of commands required to produce that data.frame. Each row of the data.frame should correspond to a row of the SummarizedExperiment.

For documentation:

• .definePanelTour(x) returns an data.frame containing the steps of a panel-specific tour.

Unless explicitly specialized above, all methods from the parent class Panel are also available.

Author(s)

Aaron Lun

Examples

#################
# For end-users #
#################

x <- RowDataTable()
x[["Selected"]]
x[["Selected"]] <- "SOME_ROW_NAME"

##################
# For developers #
##################

library(scater)
sce <- mockSCE()

# Sets the search columns appropriately.
sce <- .cacheCommonInfo(x, sce)
.refineParameters(x, sce)

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The RowDotPlot virtual class

Description

The RowDotPlot is a virtual class where each row in the SummarizedExperiment is represented by no more than one point (i.e., a “dot”) in a brushable ggplot plot. It provides slots and methods to extract rowData fields to control the per-point aesthetics on the plot. This panel will transmit row identities in both its single and multiple selections, and it can receive multiple row selections but not multiple column selections.

Slot overview

The following slots control coloring of the points:

• ColorByRowData, a string specifying the rowData field for controlling point color, if ColorBy="Row data" (see the Panel class). Defaults to the first valid field (see .cacheCommonInfo below).

• ColorBySampleNameAssay, a string specifying the assay of the SummarizedExperiment object containing values to use for coloring, if ColorBy="Sample name". Defaults to "logcounts" in getPanelDefault, falling back to the name of the first valid assay (see ?".cacheCommonInfo,DotPlot-method" for the definition of validity).

• ColorByFeatureNameColor, a string specifying the color to use for coloring an individual sample on the plot, if ColorBy="Feature name". Defaults to "red" in getPanelDefault.

The following slots control other metadata-related aesthetic aspects of the points:

• ShapeByRowData, a string specifying the rowData field for controlling point shape, if ShapeBy="Row data" (see the Panel class). The specified field should contain categorical values; defaults to the first such field.

• SizeByRowData, a string specifying the rowData field for controlling point size, if SizeBy="Row data" (see the Panel class). The specified field should contain continuous values; defaults to the first such field.

• TooltipRowData, a character vector specifying rowData fields to show in the tooltip. Defaults to 'character(0)', which displays only the 'rownames' value of the data point.

In addition, this class inherits all slots from its parent DotPlot and Panel classes.

Supported methods

In the following code snippets, x is an instance of a RowDotPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

• .cacheCommonInfo(x) adds a "RowDotPlot" entry containing valid.rowData.names, a character vector of valid column data names (i.e., containing atomic values); discrete.rowData.names, a character vector of names for discrete columns; and continuous.rowData.names, a character vector of names of continuous columns. This will also call the equivalent DotPlot method.

• .refineParameters(x, se) replaces NA values in ColorByFeatAssay with the first valid assay name in se. This will also call the equivalent DotPlot method.

For defining the interface:

• .hideInterface(x, field) returns a logical scalar indicating whether the interface element corresponding to field should be hidden. This returns TRUE for row selection parameters ("RowSelectionSource" and "RowSelectionRestrict"), otherwise it dispatches to the Panel method.

For monitoring reactive expressions:

• .createObservers(x, se, input, session, pObjects, rObjects) sets up observers for all slots in the RowDotPlot. This will also call the equivalent DotPlot method.

For controlling selections:

• .multiSelectionRestricted(x) returns a logical scalar indicating whether x is restricting the plotted points to those that were selected in a transmitting panel.

• .multiSelectionDimension(x) returns "row" to indicate that a multiple row selection is being transmitted.

• .multiSelectionInvalidated(x) returns TRUE if the faceting options use the multiple row selections, such that the point coordinates/domain may change upon updates to upstream selections in transmitting panels.

• .singleSelectionDimension(x) returns "feature" to indicate that a feature identity is being transmitted.

For documentation:

• .definePanelTour(x) returns an data.frame containing the steps of a tour relevant to subclasses, mostly tuning the more generic descriptions from the same method of the parent DotPlot.

• .getDotPlotColorHelp(x, color_choices) returns a data.frame containing the documentation for the "ColorBy" UI element, specialized for row-based dot plots.

Unless explicitly specialized above, all methods from the parent classes DotPlot and Panel are also available.

Subclass expectations

Subclasses are expected to implement methods for, at least:

• .generateDotPlotData

• .fullName

• .panelColor

The method for .generateDotPlotData should create a plot.data data.frame with one row per row in the SummarizedExperiment object.

Author(s)

Aaron Lun

See Also

DotPlot, for the immediate parent class that contains the actual slot definitions.

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