Package 'InteractiveComplexHeatmap' reference manual

Title:	Make Interactive Complex Heatmaps
Description:	This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.
Authors:	Zuguang Gu [aut, cre]
Maintainer:	Zuguang Gu <[email protected]>
License:	MIT + file LICENSE
Version:	1.13.0
Built:	2024-06-30 04:16:12 UTC
Source:	https://github.com/bioc/InteractiveComplexHeatmap

Get all column indicies from the selected data frame

Description

Get all column indicies from the selected data frame

Usage

all_column_indices(df)
all_column_indices(df)

Arguments

`df`	The selected data frame.

Examples

# There is no example
NULL

# There is no example
NULL

Get all row indicies from the selected data frame

Description

Get all row indicies from the selected data frame

Usage

all_row_indices(df)
all_row_indices(df)

Arguments

`df`	The selected data frame.

Examples

# There is no example
NULL

# There is no example
NULL

Get the position of the brushed area on the heatmap image

Description

Get the position of the brushed area on the heatmap image

Usage

getPositionFromBrush(brush, ratio = 1)
getPositionFromBrush(brush, ratio = 1)

Arguments

`brush`	The input brush object. Assume `heatmap_brush` is the ID set to argument `brush` in `plotOutput`, then the value here is `input$heatmap_brush`.
`ratio`	The relative resolution. The value should the ratio between `res` set in `makeInteractiveComplexHeatmap` and 72 (`res/72`).

Value

A list of length two. The two elements correspons to the coordinates of the two diagonal points.

Examples

# There is no example
NULL

# There is no example
NULL

Get the position of clicked point on the heatmap image

Description

Get the position of clicked point on the heatmap image

Usage

getPositionFromClick(click, ratio = 1)
getPositionFromClick(click, ratio = 1)

Arguments

`click`	The input click object. Assume `heatmap_click` is the ID set to argument `click` in `plotOutput`, then the value here is `input$heatmap_click`.
`ratio`	The relative resolution. The value should the ratio between `res` set in `makeInteractiveComplexHeatmap` and 72 (`res/72`).

Value

A unit object of length two which are the coordinates of the clicked points.

Examples

# There is no example
NULL

# There is no example
NULL

Get the position of double clicked point on the heatmap image

Description

Get the position of double clicked point on the heatmap image

Usage

getPositionFromDblclick(dblclick, ratio = 1)
getPositionFromDblclick(dblclick, ratio = 1)

Arguments

`dblclick`	The input dblclick object. Assume `heatmap_dblclick` is the ID set to argument `dblclick` in `plotOutput`, then the value here is `input$heatmap_dblclick`.
`ratio`	The relative resolution. The value should the ratio between `res` set in `makeInteractiveComplexHeatmap` and 72 (`res/72`).

Value

A unit object of length two which are the coordinates of the double clicked points.

Examples

# There is no example
NULL

# There is no example
NULL

Get the position of hovered point on the heatmap image

Description

Get the position of hovered point on the heatmap image

Usage

getPositionFromHover(hover, ratio = 1)
getPositionFromHover(hover, ratio = 1)

Arguments

`hover`	The input hover object. Assume `heatmap_hover` is the ID set to argument `hover` in `plotOutput`, then the value here is `input$heatmap_hover`.
`ratio`	The relative resolution. The value should the ratio between `res` set in `makeInteractiveComplexHeatmap` and 72 (`res/72`).

Value

A unit object of length two which are the coordinates of the hover points.

Examples

# There is no example
NULL

# There is no example
NULL

UI for the output

Description

UI for the output

Usage

HeatmapInfoOutput(heatmap_id, title = NULL, width = 400,
    output_ui = default_output_ui(heatmap_id),
    output_ui_float = FALSE, action = NULL, response = NULL, internal = FALSE)
HeatmapInfoOutput(heatmap_id, title = NULL, width = 400,
    output_ui = default_output_ui(heatmap_id),
    output_ui_float = FALSE, action = NULL, response = NULL, internal = FALSE)

Arguments

`heatmap_id`	ID of the plot.
`title`	Title of the output.
`width`	Width of the output div.
`output_ui`	A `htmlOutput` or other `*Output` object (defined in shiny or other related packages).
`output_ui_float`	Whether the UI defined by `output_ui` floats at the mouse positions.
`action`	It is only used when `output_ui_float = TRUE` to properly bind the floating frame to the event on heatmap (i.e. `click`, `hover` or `dblclick`). If `HeatmapInfoOutput` is executed after `originalHeatmapOutput`, the value for it is automatically decided
`response`	It is only used when `output_ui_float = TRUE` and `response = "brush"` or `response = "brush-output"`, so that single clicking or hovering won't have any effect, in other word, there is only response from brushing. If `HeatmapInfoOutput` is executed after `originalHeatmapOutput`, the value for it is automatically decided
`internal`	Internally used.

Examples

# See examples on the help page of originalHeatmapOutput()
# See examples on the help page of originalHeatmapOutput()

Interactive heatmaps as a Shiny app

Description

Interactive heatmaps as a Shiny app

Usage

ht_shiny(...)
ht_shiny(...)

Arguments

...

All goes to htShiny.

Value

A Shiny app object.

Examples

# There is no example
NULL

# There is no example
NULL

Get heatmap positions on the graphics device

Description

Get heatmap positions on the graphics device

Usage

htPositionsOnDevice(ht_list = get_last_ht(), unit = "inch", valueOnly = FALSE,
    include_annotation = FALSE, calibrate = TRUE)
htPositionsOnDevice(ht_list = get_last_ht(), unit = "inch", valueOnly = FALSE,
    include_annotation = FALSE, calibrate = TRUE)

Arguments

`ht_list`	A `HeatmapList-class` object returned by `draw,Heatmap-method` or `draw,HeatmapList-method`. If it is omitted, it uses the last generated heatmap.
`unit`	The unit.
`valueOnly`	Whether only return the numeric values.
`include_annotation`	Internally used.
`calibrate`	Internally used.

Details

ht_list must have been already updated by draw() function. The function needs to be executed under a graphics device where the heatmap is written.

Value

It returns a DataFrame object of the position of every heatmap slice.

Examples

if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    ht = Heatmap(m, row_km = 2, column_km = 2)
    ht = draw(ht)
    pos = htPositionsOnDevice(ht)

    InteractiveComplexHeatmap:::redraw_ht_vp(pos)
}
if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    ht = Heatmap(m, row_km = 2, column_km = 2)
    ht = draw(ht)
    pos = htPositionsOnDevice(ht)

    InteractiveComplexHeatmap:::redraw_ht_vp(pos)
}

Interactive heatmaps as a Shiny app

Description

Interactive heatmaps as a Shiny app

Usage

htShiny(ht_list = get_last_ht(), title = NULL,
    description = NULL, hline = TRUE, html = NULL,
    
    # parameters passed to InteractiveComplexHeatmapOutput()
    heatmap_id = NULL, title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 400,
    height2 = 350,
    width3 = ifelse(layout == "(1-2)|3", 800, 400),
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE, response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui_float = FALSE,
    
    # specific for sub-heatmap
    show_cell_fun = TRUE, show_layer_fun = TRUE,
    
    save = NULL, app_options = list())
htShiny(ht_list = get_last_ht(), title = NULL,
    description = NULL, hline = TRUE, html = NULL,
    
    # parameters passed to InteractiveComplexHeatmapOutput()
    heatmap_id = NULL, title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 400,
    height2 = 350,
    width3 = ifelse(layout == "(1-2)|3", 800, 400),
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE, response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui_float = FALSE,
    
    # specific for sub-heatmap
    show_cell_fun = TRUE, show_layer_fun = TRUE,
    
    save = NULL, app_options = list())

Arguments

`ht_list`	A `Heatmap-class` or a `HeatmapList-class` object. If it is not specified, the last generated heatmap is used. The heatmap object should better be already updated by `draw()` function.
`title`	Title of the app.
`description`	Description of the app. The content will be wrapped by a `p` tag and inserted before the interactive heatmap widget.
`hline`	Whether to add the horizontal line (by `hr` tag) after `description`.
`html`	HTML fragment inserted below the heatmap. The value can be a string or be wrapped by `HTML`.
`heatmap_id`	Pass to `InteractiveComplexHeatmapOutput`.
`title1`	Pass to `InteractiveComplexHeatmapOutput`.
`title2`	Pass to `InteractiveComplexHeatmapOutput`.
`width1`	Pass to `InteractiveComplexHeatmapOutput`.
`height1`	Pass to `InteractiveComplexHeatmapOutput`.
`width2`	Pass to `InteractiveComplexHeatmapOutput`.
`height2`	Pass to `InteractiveComplexHeatmapOutput`.
`width3`	Pass to `InteractiveComplexHeatmapOutput`.
`layout`	Pass to `InteractiveComplexHeatmapOutput`.
`compact`	Pass to `InteractiveComplexHeatmapOutput`.
`action`	Pass to `InteractiveComplexHeatmapOutput`.
`cursor`	Pass to `InteractiveComplexHeatmapOutput`.
`response`	Pass to `InteractiveComplexHeatmapOutput`.
`brush_opt`	Pass to `InteractiveComplexHeatmapOutput`.
`output_ui_float`	Pass to `InteractiveComplexHeatmapOutput`.
`show_cell_fun`	Whether show graphics made by `cell_fun` on the main heatmap?
`show_layer_fun`	Whether show graphics made by `cell_fun` on the main heatmap?
`save`	The value can be set to a folder name so that the shiny app is saved into several files.
`app_options`	All pass to the `options` argument in `shinyApp`.

Details

With any Heatmap/HeatmapList object, directly send to htShiny() to create a Shiny app for the heatmap(s):

    htShiny(ht_list)

If the heatmaps are already drawn, ht_list can be omitted and the last heatmap object is retrieved automatically:

    Heatmap(...) + other_heatmaps_or_annotations # or other functions that internally use Heatmap()
    htShiny()

Value

A Shiny app object.

Examples

# use last generated heatmap
if(interactive() && dev.interactive()) {
    m = matrix(rnorm(100), 10)
    Heatmap(m)
    htShiny()
}

# by providing a heatmap/heatmap list
if(interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    htShiny(ht)
}

# vertical heatmap list
if(interactive()) {
    m1 = matrix(rnorm(100), 10)
    rownames(m1) = 1:10
    colnames(m1) = 1:10
    ht1 = Heatmap(m1, row_km = 2, column_km = 2)

    m2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10)
    ht2 = Heatmap(m2)

    ht_list = draw(ht1 + ht2)
    htShiny(ht_list)

    ht_list = ht1 %v% ht2
    htShiny(ht_list)
}

# compact mode
if(interactive()) {
    m = matrix(rnorm(100), 10)
    Heatmap(m)
    htShiny(compact = TRUE)
}
# use last generated heatmap
if(interactive() && dev.interactive()) {
    m = matrix(rnorm(100), 10)
    Heatmap(m)
    htShiny()
}

# by providing a heatmap/heatmap list
if(interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    htShiny(ht)
}

# vertical heatmap list
if(interactive()) {
    m1 = matrix(rnorm(100), 10)
    rownames(m1) = 1:10
    colnames(m1) = 1:10
    ht1 = Heatmap(m1, row_km = 2, column_km = 2)

    m2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10)
    ht2 = Heatmap(m2)

    ht_list = draw(ht1 + ht2)
    htShiny(ht_list)

    ht_list = ht1 %v% ht2
    htShiny(ht_list)
}

# compact mode
if(interactive()) {
    m = matrix(rnorm(100), 10)
    Heatmap(m)
    htShiny(compact = TRUE)
}

Examples of interactive complex heatmaps

Description

Examples of interactive complex heatmaps

Usage

htShinyExample(which)
htShinyExample(which)

Arguments

which

An index of which example to use. The list of all examples can be obtained by executing htShinyExample with no argument.

Details

In every example, there is a Shiny app opened, which also includes source code that generates this app.

Value

A Shiny app object.

Examples

# list all examples
htShinyExample()

if(interactive()) {
    htShinyExample(4.2)
}
# list all examples
htShinyExample()

if(interactive()) {
    htShinyExample(4.2)
}

Generic function for interactivate an object in an interactive Shiny app

Description

Generic function for interactivate an object in an interactive Shiny app

Usage

interactivate(x, ...)
interactivate(x, ...)

Arguments

`x`	An object.
`...`	Other arguments.

Examples

# There is no example
NULL

# There is no example
NULL

Visualize DESeq2 result in an interactive Shiny app

Description

Visualize DESeq2 result in an interactive Shiny app

Usage

## S3 method for class 'DESeqDataSet'
interactivate(x, res = DESeq2::results(x), seed = 123, ...)
## S3 method for class 'DESeqDataSet'
interactivate(x, res = DESeq2::results(x), seed = 123, ...)

Arguments

`x`	A `DESeqDataSet` class object. It is normally returned by `DESeq`.
`res`	The object returned by `results`.
`seed`	Random seed. It is mainly set for the random colors of annotations.
`...`	Other arguments.

Examples

if(interactive()) {
    require(airway)
    data(airway)
    se = airway

    require(DESeq2)
    dds = DESeqDataSet(se, design = ~ dex)
    keep = rowSums(counts(dds)) >= 10
    dds = dds[keep, ]
    dds$dex = relevel(dds$dex, ref = "untrt")
    dds = DESeq(dds)

    interactivate(dds)
}
if(interactive()) {
    require(airway)
    data(airway)
    se = airway

    require(DESeq2)
    dds = DESeqDataSet(se, design = ~ dex)
    keep = rowSums(counts(dds)) >= 10
    dds = dds[keep, ]
    dds$dex = relevel(dds$dex, ref = "untrt")
    dds = DESeq(dds)

    interactivate(dds)
}

Interactive Shiny application for 2D density distribution

Description

Interactive Shiny application for 2D density distribution

Usage

## S3 method for class 'kde'
interactivate(x, ...)
## S3 method for class 'kde'
interactivate(x, ...)

Arguments

`x`	a `kde` object generated by `kde`.
`...`	Other arguments.

Examples

if(interactive()) {
    require(ks)
    lt = readRDS(system.file("extdata", "2d_density_xy.rds", package = "InteractiveComplexHeatmap"))
    data = cbind(lt$x, lt$y)
    fit = kde(data)
    interactivate(fit)
}
if(interactive()) {
    require(ks)
    lt = readRDS(system.file("extdata", "2d_density_xy.rds", package = "InteractiveComplexHeatmap"))
    data = cbind(lt$x, lt$y)
    fit = kde(data)
    interactivate(fit)
}

Interactive Shiny application for 2D density distribution

Description

Interactive Shiny application for 2D density distribution

Usage

interactivateDensity2D(x, y, ...)
interactivateDensity2D(x, y, ...)

Arguments

`x`	A numeric vector.
`y`	A numeric vector.
`...`	All pass to `kde`.

Examples

if(interactive()) {
    lt = readRDS(system.file("extdata", "2d_density_xy.rds", package = "InteractiveComplexHeatmap"))
    interactivateDensity2D(lt$x, lt$y)
}
if(interactive()) {
    lt = readRDS(system.file("extdata", "2d_density_xy.rds", package = "InteractiveComplexHeatmap"))
    interactivateDensity2D(lt$x, lt$y)
}

Interactive complex heatmap modal dialog

Description

Interactive complex heatmap modal dialog

Usage

InteractiveComplexHeatmapModal(
    input, output, session, ht_list, heatmap_id = NULL,
    
    # parameters passed to InteractiveComplexHeatmapOutput()
    title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 370,
    height2 = 350,
    width3 = ifelse(layout == "(1-2)|3", 800, 370),
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE, response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui = TRUE, output_ui_float = FALSE,
    
    # parameters passed to makeInteractiveComplexHeatmap()
    click_action = NULL, brush_action = NULL,
    
    # other configurations
    js_code = "", close_button = TRUE, cancel_action = c("remove", "hide"))
InteractiveComplexHeatmapModal(
    input, output, session, ht_list, heatmap_id = NULL,
    
    # parameters passed to InteractiveComplexHeatmapOutput()
    title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 370,
    height2 = 350,
    width3 = ifelse(layout == "(1-2)|3", 800, 370),
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE, response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui = TRUE, output_ui_float = FALSE,
    
    # parameters passed to makeInteractiveComplexHeatmap()
    click_action = NULL, brush_action = NULL,
    
    # other configurations
    js_code = "", close_button = TRUE, cancel_action = c("remove", "hide"))

Arguments

`input`	Passed from the Shiny server function.
`output`	Passed from the Shiny server function.
`session`	Passed from the Shiny server function.
`ht_list`	A `Heatmap-class` or a `HeatmapList-class` object.
`heatmap_id`	ID of the plot. If it is not specified, an internal ID is assigned.
`title1`	Pass to `InteractiveComplexHeatmapOutput`.
`title2`	Pass to `InteractiveComplexHeatmapOutput`.
`width1`	Pass to `InteractiveComplexHeatmapOutput`.
`height1`	Pass to `InteractiveComplexHeatmapOutput`.
`width2`	Pass to `InteractiveComplexHeatmapOutput`.
`height2`	Pass to `InteractiveComplexHeatmapOutput`.
`width3`	Pass to `InteractiveComplexHeatmapOutput`.
`layout`	Pass to `InteractiveComplexHeatmapOutput`.
`compact`	Pass to `InteractiveComplexHeatmapOutput`.
`action`	Pass to `InteractiveComplexHeatmapOutput`.
`cursor`	Pass to `InteractiveComplexHeatmapOutput`.
`response`	Pass to `InteractiveComplexHeatmapOutput`.
`brush_opt`	Pass to `InteractiveComplexHeatmapOutput`.
`output_ui`	Pass to `InteractiveComplexHeatmapOutput`.
`output_ui_float`	Pass to `InteractiveComplexHeatmapOutput`.
`click_action`	Pass to `makeInteractiveComplexHeatmap`.
`brush_action`	Pass to `makeInteractiveComplexHeatmap`.
`js_code`	Additional JavaScript code that is put after the interactive heatmap UI. The value can be a text or a function that takes "heatmap ID" as the argument and returns the formatted JavaScript code.
`close_button`	Whether to add a close button at the end of the widget. If it is `FALSE`, the widget can be closed by clicking outside of the widget.
`cancel_action`	Whether to remove the UI from HTML or just hide it when the UI is closed.

Details

It creates an interactive heatmap "modal dialog" according to a certain action.

The function is normally put inside observe or observeEvent.

Value

No value is returned.

Examples

if(interactive()) {
    require(ComplexHeatmap)

    ui = fluidPage(
        actionButton("show_heatmap", "Generate_heatmap"),
    )

    server = function(input, output, session) {
        m = matrix(rnorm(100), 10)
        ht = Heatmap(m)

        observeEvent(input$show_heatmap, {
            InteractiveComplexHeatmapModal(input, output, session, ht)
        })
    }
    shiny::shinyApp(ui, server)
}
if(interactive()) {
    require(ComplexHeatmap)

    ui = fluidPage(
        actionButton("show_heatmap", "Generate_heatmap"),
    )

    server = function(input, output, session) {
        m = matrix(rnorm(100), 10)
        ht = Heatmap(m)

        observeEvent(input$show_heatmap, {
            InteractiveComplexHeatmapModal(input, output, session, ht)
        })
    }
    shiny::shinyApp(ui, server)
}

UI for the interactive complex heatmaps

Description

UI for the interactive complex heatmaps

Usage

InteractiveComplexHeatmapOutput(heatmap_id = NULL,
    title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    title3 = if(output_ui_float) NULL else "Output",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 400,
    height2 = 350,
    width3 = NULL,
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE,
    response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui = default_output_ui(heatmap_id),
    output_ui_float = FALSE, containment = FALSE,
    internal = FALSE,
    ...)
InteractiveComplexHeatmapOutput(heatmap_id = NULL,
    title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    title3 = if(output_ui_float) NULL else "Output",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 400,
    height2 = 350,
    width3 = NULL,
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE,
    response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui = default_output_ui(heatmap_id),
    output_ui_float = FALSE, containment = FALSE,
    internal = FALSE,
    ...)

Arguments

`heatmap_id`	ID of the plot. If it is not specified, an internal ID is assigned.
`title1`	Title of the original heatmap.
`title2`	Title of the sub-heatmap.
`title3`	Title of the output.
`width1`	Width of the original heatmap.
`height1`	Height of the original heatmap.
`width2`	Width of the sub-heatmap.
`height2`	Height of the sub-heatmap.
`width3`	Width of the output div.
`layout`	One of `"(1\|2)-3"`, `"1-(2\|3)"`, `"1-2-3"`, `"1\|2\|3"`, `"1\|(2-3)"`. If `brush` is not set with the argument `response`, which means there is no sub-heatmap panel, the code `2` can be omitted.
`compact`	If the value is `TRUE`, there will be no sub-heatmap, and output floats at the mouse position when click/hover on the original heatmap.
`action`	Which action for selecting single cells on the heatmap? Value should be `click`, `hover` or `dblclick`.
`cursor`	When moving mouse on heatmap, whether to show the cursors on the four sides?
`response`	Which action needs to be responded on the server side? Value should be in `click`/`hover`/`dblclick`, `brush` and `brush-output`. `brush` responds in two places which are the sub-heatmap and the output components and `brush-output` only responds in the output component.
`brush_opt`	A list of parameters passed to `brushOpts`. Do not set an ID for the brush. An internal brush ID is automatically set.
`output_ui`	A `htmlOutput` or other `*Output` object (defined in shiny or other related packages). If it is set to `NULL`, there is no output component in the app.
`output_ui_float`	Whether the UI defined by `output_ui` floats at the mouse positions.
`containment`	Whether the resizing is restricted in a certain parent div? Value can be `TRUE`/`FALSE` or a JQuery selector.
`internal`	Internally used.
`...`	Pass to the UI container which is wrapped by `fluidPage`.

Details

This function generates HTML fragment for the interactive UI. See the example in makeInteractiveComplexHeatmap page.

layout is defined as follows (1 for the original heatmap, 2 for the selected sub-heatmap and 3 is for the output:

"(1-2)|3": Heatmap and sub-heatmap are in a same row, and output is in a second row. This is the default layout.
"1|(2-3)": Heatmap is in a single row, while sub-heatmap and output are in a second row.
"1-2-3": All three components are in a same row.
"1|2|3": Each component is in a single row.
"1-(2|3)": Being different from the other four layouts, this is a two-column layout. Heatmap is in a sigle column. Sub-heatmap and output are vertically aligned and the two are in the second column.

The hover event is implemented with https://github.com/websanova/mousestop .

Value

A UI that can be used in Shiny.

Examples

# There is no example
NULL

# There is no example
NULL

Interactive complex heatmap widget

Description

Interactive complex heatmap widget

Usage

InteractiveComplexHeatmapWidget(
    input, output, session, ht_list, heatmap_id = NULL, output_id,
    
    # parameters passed to InteractiveComplexHeatmapOutput()
    title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 370,
    height2 = 350,
    width3 = ifelse(layout == "(1-2)|3", 800, 370),
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE, response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui = TRUE, output_ui_float = FALSE,
    
    # parameters passed to makeInteractiveComplexHeatmap()
    click_action = NULL, brush_action = NULL,
    
    # other configurations
    js_code = "", close_button = TRUE, cancel_action = c("remove", "hide"))
InteractiveComplexHeatmapWidget(
    input, output, session, ht_list, heatmap_id = NULL, output_id,
    
    # parameters passed to InteractiveComplexHeatmapOutput()
    title1 = "Original heatmap", title2 = "Selected sub-heatmap",
    width1 = ifelse(layout == "1|(2-3)", 800, 450),
    height1 = ifelse(layout == "1-(2|3)", 700, 350),
    width2 = 370,
    height2 = 350,
    width3 = ifelse(layout == "(1-2)|3", 800, 370),
    layout = ifelse("brush" %in% response, "(1-2)|3", "1-3"), compact = FALSE,
    action = "click", cursor = TRUE, response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    output_ui = TRUE, output_ui_float = FALSE,
    
    # parameters passed to makeInteractiveComplexHeatmap()
    click_action = NULL, brush_action = NULL,
    
    # other configurations
    js_code = "", close_button = TRUE, cancel_action = c("remove", "hide"))

Arguments

`input`	Passed from the Shiny server function.
`output`	Passed from the Shiny server function.
`session`	Passed from the Shiny server function.
`ht_list`	A `Heatmap-class` or a `HeatmapList-class` object.
`heatmap_id`	ID of the plot. If it is not specified, an internal ID is assigned.
`output_id`	Where the heatmap is put.
`title1`	Pass to `InteractiveComplexHeatmapOutput`.
`title2`	Pass to `InteractiveComplexHeatmapOutput`.
`width1`	Pass to `InteractiveComplexHeatmapOutput`.
`height1`	Pass to `InteractiveComplexHeatmapOutput`.
`width2`	Pass to `InteractiveComplexHeatmapOutput`.
`height2`	Pass to `InteractiveComplexHeatmapOutput`.
`width3`	Pass to `InteractiveComplexHeatmapOutput`.
`layout`	Pass to `InteractiveComplexHeatmapOutput`.
`compact`	Pass to `InteractiveComplexHeatmapOutput`.
`action`	Pass to `InteractiveComplexHeatmapOutput`.
`cursor`	Pass to `InteractiveComplexHeatmapOutput`.
`response`	Pass to `InteractiveComplexHeatmapOutput`.
`brush_opt`	Pass to `InteractiveComplexHeatmapOutput`.
`output_ui`	Pass to `InteractiveComplexHeatmapOutput`.
`output_ui_float`	Pass to `InteractiveComplexHeatmapOutput`.
`click_action`	Pass to `makeInteractiveComplexHeatmap`.
`brush_action`	Pass to `makeInteractiveComplexHeatmap`.
`js_code`	Additional JavaScript code that is put after the interactive heatmap UI. The value can be a text or a function that takes "heatmap ID" as the argument and returns the formatted JavaScript code.
`close_button`	Whether to add a close button at the end of the widget.
`cancel_action`	Whether to remove the UI from HTML or just hide it when the UI is closed.

Details

It creates an interactive heatmap widget according to a certain action. The UI is placed to the output ID that user defined.

The function is normally put inside observe or observeEvent.

Value

No value is returned.

Examples

if(interactive()) {
    require(ComplexHeatmap)

    ui = fluidPage(
        actionButton("show_heatmap", "Generate_heatmap"),
        htmlOutput("heatmap_output")
    )

    server = function(input, output, session) {
        m = matrix(rnorm(100), 10)
        ht = Heatmap(m)

        observeEvent(input$show_heatmap, {
            InteractiveComplexHeatmapWidget(input, output, session, ht, 
                output_id = "heatmap_output")
        })
    }
    shiny::shinyApp(ui, server)
}
if(interactive()) {
    require(ComplexHeatmap)

    ui = fluidPage(
        actionButton("show_heatmap", "Generate_heatmap"),
        htmlOutput("heatmap_output")
    )

    server = function(input, output, session) {
        m = matrix(rnorm(100), 10)
        ht = Heatmap(m)

        observeEvent(input$show_heatmap, {
            InteractiveComplexHeatmapWidget(input, output, session, ht, 
                output_id = "heatmap_output")
        })
    }
    shiny::shinyApp(ui, server)
}

Test whether it is in sub heatmap

Description

Test whether it is in sub heatmap

Usage

is_in_sub_heatmap()
is_in_sub_heatmap()

Details

Normally, it is used in cell_fun/layer_fun.

Examples

# There is no example
NULL

# There is no example
NULL

Process heatmaps on the sever side

Description

Process heatmaps on the sever side

Usage

makeInteractiveComplexHeatmap(input, output, session, ht_list,
    heatmap_id = shiny_env$current_heatmap_id,
    click_action = NULL, hover_action = NULL,
    dblclick_action = NULL, brush_action = NULL, res = 72,
    show_cell_fun = TRUE, show_layer_fun = TRUE)
makeInteractiveComplexHeatmap(input, output, session, ht_list,
    heatmap_id = shiny_env$current_heatmap_id,
    click_action = NULL, hover_action = NULL,
    dblclick_action = NULL, brush_action = NULL, res = 72,
    show_cell_fun = TRUE, show_layer_fun = TRUE)

Arguments

`input`	Passed from the Shiny server function.
`output`	Passed from the Shiny server function.
`session`	Passed from the Shiny server function.
`ht_list`	A `Heatmap-class` or a `HeatmapList-class` object.
`heatmap_id`	The corresponding heatmap ID from the UI. If there is only one interactive heatmap in the app, this argument does not need to be specified and it will use the current one used in `InteractiveComplexHeatmapOutput`.
`click_action`	Additional actions on the server side when receiving a click event on the UI. This self-defined function should accept two or four arguments. If it is two arguments, they should be `df` and `output` and if it is four arguments, they should be `df`, `input`, `output` and `session`.
`hover_action`	Additional actions at the server side when receiving a hover event on the UI.
`dblclick_action`	Additional actions at the server side when receiving a dblclick event on the UI.
`brush_action`	Additional actions at the server side when receiving a brush event on the UI.
`res`	Resolution of the plot, pass to `renderPlot`.
`show_cell_fun`	Whether show graphics made by `cell_fun` on the main heatmap?
`show_layer_fun`	Whether show graphics made by `cell_fun` on the main heatmap?

Value

No value is returned.

Examples

if(interactive()) {
    ht = Heatmap(m)
    ht = draw(ht)

    ui = fluidPage(
        InteractiveComplexHeatmapOutput()
    )

    server = function(input, output, session) {
        makeInteractiveComplexHeatmap(input, output, session, ht)
    }

    shiny::shinyApp(ui, server)
}
if(interactive()) {
    ht = Heatmap(m)
    ht = draw(ht)

    ui = fluidPage(
        InteractiveComplexHeatmapOutput()
    )

    server = function(input, output, session) {
        makeInteractiveComplexHeatmap(input, output, session, ht)
    }

    shiny::shinyApp(ui, server)
}

UI for the original heatmap

Description

UI for the original heatmap

Usage

originalHeatmapOutput(heatmap_id, title = NULL,
    width = 450, height = 350,
    action = "click", cursor = TRUE,
    response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    containment = FALSE, internal = FALSE)
originalHeatmapOutput(heatmap_id, title = NULL,
    width = 450, height = 350,
    action = "click", cursor = TRUE,
    response = c(action, "brush"),
    brush_opt = list(stroke = "#f00", opacity = 0.6),
    containment = FALSE, internal = FALSE)

Arguments

`heatmap_id`	ID of the plot.
`title`	Title of the original heatmap.
`width`	Width of the original heatmap.
`height`	Height of the original heatmap.
`action`	Which action for selecting single cells on the heatmap? Value should be `click`, `hover` or `dblclick`.
`cursor`	When moving mouse on heatmap, whether to show the cursors on the four sides?
`response`	Which action needs to be responded on the server side? Value should be in `click`/`hover`/`dblclick`, `brush` and `brush-output`. `brush` responds in two places which are the sub-heatmap and the output components and `brush-output` only responds in the output component.
`brush_opt`	A list of parameters passed to `brushOpts`. Do not set an ID for the brush. An internal brush ID is automatically set.
`containment`	Whether the resizing is restricted in a certain parent div? Value can be `TRUE`/`FALSE` or a JQuery selector.
`internal`	Internally used.

Examples

if(interactive()) {
    require(shinydashboard)
    m = matrix(rnorm(100), 10)
    ht = Heatmap(m)

    body = dashboardBody(
        fluidRow(
            box(title = "Original heatmap", width = 4, solidHeader = TRUE, status = "primary",
                originalHeatmapOutput("ht")
            ),
            box(title = "Sub-heatmap", width = 4, solidHeader = TRUE, status = "primary",
                subHeatmapOutput("ht")
            ),
            box(title = "Output", width = 4, solidHeader = TRUE, status = "primary",
                HeatmapInfoOutput("ht")
            )
        )
    )
    ui = dashboardPage(
        dashboardHeader(),
        dashboardSidebar(),
        body
    )
    server = function(input, output, session) {
        makeInteractiveComplexHeatmap(input, output, session, ht, "ht")
    }
    shinyApp(ui, server)
}
if(interactive()) {
    require(shinydashboard)
    m = matrix(rnorm(100), 10)
    ht = Heatmap(m)

    body = dashboardBody(
        fluidRow(
            box(title = "Original heatmap", width = 4, solidHeader = TRUE, status = "primary",
                originalHeatmapOutput("ht")
            ),
            box(title = "Sub-heatmap", width = 4, solidHeader = TRUE, status = "primary",
                subHeatmapOutput("ht")
            ),
            box(title = "Output", width = 4, solidHeader = TRUE, status = "primary",
                HeatmapInfoOutput("ht")
            )
        )
    )
    ui = dashboardPage(
        dashboardHeader(),
        dashboardSidebar(),
        body
    )
    server = function(input, output, session) {
        makeInteractiveComplexHeatmap(input, output, session, ht, "ht")
    }
    shinyApp(ui, server)
}

A random matrix

Description

A random matrix

Usage

data(rand_mat)
data(rand_mat)

Details

Following code was used to generate rand_mat:

  set.seed(123)
  rand_mat = cbind(rbind(matrix(rnorm(20*20, mean = 1, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20)),
            rbind(matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 1, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0, sd = 0.5), nr = 20)),
            rbind(matrix(rnorm(20*20, mean = 0.5, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 0.5, sd = 0.5), nr = 20),
                  matrix(rnorm(20*20, mean = 1, sd = 0.5), nr = 20))
           ) + matrix(rnorm(60*60, sd = 0.5), nr = 60)
   colnames(rand_mat) = paste0("C", 1:60)
   rownames(rand_mat) = paste0("R", 1:60)

Author(s)

Zuguang Gu <[email protected]>

Examples

data(rand_mat)
rand_mat
data(rand_mat)
rand_mat

Record the observation object

Description

Record the observation object

Usage

record_observation(obs, heatmap_id = shiny_env$current_heatmap_id)
record_observation(obs, heatmap_id = shiny_env$current_heatmap_id)

Arguments

`obs`	Observation object returned by `observe` or `observeEvent`.
`heatmap_id`	The Heatmap ID.

Examples

# There is no example
NULL

# There is no example
NULL

Select an area in the heatmap

Description

Select an area in the heatmap

Usage

selectArea(ht_list = get_last_ht(), pos1 = NULL, pos2 = NULL, mark = TRUE, verbose = TRUE,
    ht_pos = NULL, include_annotation = FALSE, calibrate = TRUE)
selectArea(ht_list = get_last_ht(), pos1 = NULL, pos2 = NULL, mark = TRUE, verbose = TRUE,
    ht_pos = NULL, include_annotation = FALSE, calibrate = TRUE)

Arguments

`ht_list`	A `HeatmapList-class` object returned by `draw,Heatmap-method` or `draw,HeatmapList-method`. If it is omitted, it uses the last generated heatmap.
`mark`	Whether to mark the selected area as a rectangle.
`pos1`	If the value is `NULL`, it can be selected by click on the heatmap (of cource, the heatmap should be on the interactive graphics device). If it is set, it must be a `unit` object with length two which corresponds to the x and y position of the point.
`pos2`	Another point as `pos1`, together with `pos1` defines the selected region.
`verbose`	Whether to print messages.
`ht_pos`	A value returned by `htPositionsOnDevice`.
`include_annotation`	Internally used.
`calibrate`	Internally used. Mainly works for Rstudio desktop IDE.

Details

The regions can be selected interactively or selected manually by setting pos1 and pos2.

Value

A DataFrame object with row indices and column indices corresponding to the selected region.

Examples

if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    selectArea(ht)

    set.seed(123)
    ht = Heatmap(m, row_km = 2, column_km = 2)
    ht = draw(ht)
    selectArea(ht)
}
if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    selectArea(ht)

    set.seed(123)
    ht = Heatmap(m, row_km = 2, column_km = 2)
    ht = draw(ht)
    selectArea(ht)
}

Select a position in the heatmap

Description

Select a position in the heatmap

Usage

selectPosition(ht_list = get_last_ht(), pos = NULL, mark = TRUE, verbose = TRUE,
    ht_pos = NULL, calibrate = TRUE)
selectPosition(ht_list = get_last_ht(), pos = NULL, mark = TRUE, verbose = TRUE,
    ht_pos = NULL, calibrate = TRUE)

Arguments

`ht_list`	A `HeatmapList-class` object returned by `draw,Heatmap-method` or `draw,HeatmapList-method`. If it is omitted, it uses the last generated heatmap.
`mark`	Whether to mark the selected position as a point.
`pos`	If the value is `NULL`, it can be selected by click on the heatmap (of cource, the heatmap should be on the interactive graphics device). If it is set, it must be a `unit` object with length two which corresponds to the x and y position of the point.
`verbose`	Whether to print messages.
`ht_pos`	A value returned by `htPositionsOnDevice`.
`calibrate`	Internally used. Mainly works for Rstudio desktop IDE.

Details

The regions can be selected interactively or selected manually by setting pos.

Value

A DataFrame object with row indices and column indices corresponding to the selected position.

Examples

if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    selectPosition(ht)
}
if(dev.interactive()) {
    m = matrix(rnorm(100), 10)
    rownames(m) = 1:10
    colnames(m) = 1:10

    ht = Heatmap(m)
    ht = draw(ht)
    selectPosition(ht)
}

UI for the sub-heatmaps

Description

UI for the sub-heatmaps

Usage

subHeatmapOutput(heatmap_id, title = NULL,
    width = 400, height = 350, containment = FALSE, internal = FALSE)
subHeatmapOutput(heatmap_id, title = NULL,
    width = 400, height = 350, containment = FALSE, internal = FALSE)

Arguments

`heatmap_id`	ID of the plot.
`title`	Title of the sub-heatmap.
`width`	Width of the sub-heatmap.
`height`	Height of the sub-heatmap.
`containment`	Whether the resizing is restricted in a certain parent div? Value can be `TRUE`/`FALSE` or a JQuery selector.
`internal`	Internally used.

Examples

# See examples on the help page of originalHeatmapOutput()
# See examples on the help page of originalHeatmapOutput()

Package 'InteractiveComplexHeatmap'

Help Index

Get all column indicies from the selected data frame

Description

Usage

Arguments

Examples

Get all row indicies from the selected data frame

Description

Usage

Arguments

Examples

Get the position of the brushed area on the heatmap image

Description

Usage

Arguments

Value

See Also

Examples

Get the position of clicked point on the heatmap image

Description

Usage

Arguments

Value

See Also

Examples

Get the position of double clicked point on the heatmap image

Description

Usage

Arguments

Value

Examples

Get the position of hovered point on the heatmap image

Description

Usage

Arguments

Value

Examples

UI for the output

Description

Usage

Arguments

See Also

Examples

Interactive heatmaps as a Shiny app

Description

Usage

Arguments

Value

Examples

Get heatmap positions on the graphics device

Description

Usage

Arguments

Details

Value

Examples

Interactive heatmaps as a Shiny app

Description

Usage

Arguments

Details

Value

See Also

Examples

Examples of interactive complex heatmaps

Description

Usage

Arguments

Details

Value

Examples

Generic function for interactivate an object in an interactive Shiny app

Description

Usage

Arguments

Examples

Visualize DESeq2 result in an interactive Shiny app

Description

Usage