Package 'epivizrChart' reference manual

Title:	R interface to epiviz web components
Description:	This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer.
Authors:	Brian Gottfried [aut], Jayaram Kancherla [aut], Hector Corrada Bravo [aut, cre]
Maintainer:	Hector Corrada Bravo <[email protected]>
License:	Artistic-2.0
Version:	1.29.0
Built:	2024-10-31 06:20:20 UTC
Source:	https://github.com/bioc/epivizrChart

Construct URL for Websocket connection between R and UI

Description

Construct URL for Websocket connection between R and UI

Usage

.constructURL(host = "localhost", port = 7123L, path = "")
.constructURL(host = "localhost", port = 7123L, path = "")

Arguments

`host`	host
`port`	port
`path`	path

Value

url

Initialize Epiviz Chart based on chart type

Description

Initialize Epiviz Chart based on chart type

Usage

.initialize_chart(chart_type, ...)
.initialize_chart(chart_type, ...)

Arguments

`chart_type`	Chart type.
`...`	Arguments for `EpivizChart` objects.

(taken from epivizr) register epiviz actions

Description

(taken from epivizr) register epiviz actions

Usage

.register_all_the_epiviz_things(srv, app)
.register_all_the_epiviz_things(srv, app)

Arguments

`srv`	epivizrServer object
`app`	EpivizApp object

(taken from epivizr) print settings in a readable format

Description

(taken from epivizr) print settings in a readable format

Usage

.settings_as_df(chart_settings)
.settings_as_df(chart_settings)

Arguments

chart_settings

chart settings

Value

chart settings as data frame

Generic method to add navigation regions

Description

Generic method to add navigation regions

Usage

append_region(x, ...)

## S4 method for signature 'EpivizEnvironment'
append_region(x, chr, start, end, return_parent = FALSE)
append_region(x, ...)

## S4 method for signature 'EpivizEnvironment'
append_region(x, chr, start, end, return_parent = FALSE)

Arguments

`x`	an object of type `EpivizEnvironment`
`...`	other parameters
`chr`	chromosome id. ex. "chr11"
`start`	genomic region start
`end`	genomic region end
`return_parent`	To return the parent or the new navigation element. Defaults to FALSE

Example expression data from the Gene Expression barcode project

Description

See vignette data_preprocessing for code to build this object.

Usage

data(bcode_eset)
data(bcode_eset)

Format

An Biobase::ExpressionSet object

Method to add Blocks Track

Description

Method to add Blocks Track

Usage

BlocksTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
BlocksTrack(x, y, ...)
BlocksTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
BlocksTrack(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Locations of CpG Islands

Description

Locations of CpG Islands

Usage

data(cgi_gr)
data(cgi_gr)

Format

A GenomicRanges::GRanges object with locations of CpG Islands in hg19

Get default chart settings and colors

Description

Get default chart settings and colors

Usage

chart_default_settings_colors(chart_type)
chart_default_settings_colors(chart_type)

Arguments

chart_type

chart type

Value

list of settings and colors

Data container for an Epiviz Blocks Track.

Description

Data container for an Epiviz Blocks Track.

Methods

get_component_type(): Get component type for prefix of random id generator
get_default_colors(): Get default colors
get_default_settings(): Get default settings
get_name(): Get name of Epiviz Web Component

Initialize an `EpivizChart` object to visualize in viewer or knit to HTML.

Description

Initialize an EpivizChart object to visualize in viewer or knit to HTML.

Usage

epivizChart(
  data_obj = NULL,
  measurements = NULL,
  datasource_name = NULL,
  parent = NULL,
  chart = NULL,
  chr = NULL,
  start = NULL,
  end = NULL,
  settings = NULL,
  colors = NULL,
  ...
)
epivizChart(
  data_obj = NULL,
  measurements = NULL,
  datasource_name = NULL,
  parent = NULL,
  chart = NULL,
  chr = NULL,
  start = NULL,
  end = NULL,
  settings = NULL,
  colors = NULL,
  ...
)

Arguments

`data_obj`	A data object that will register to an `EpivizData` object.
`measurements`	An `EpivizMeasurement` object.
`datasource_name`	A name for the datasource. For example, "Mean by Sample Type".
`parent`	An object of class `EpivizEnvironment` or `EpivizNavigation` to append the chart within.
`chart`	The chart type to be visualized: "BlocksTrack", HeatmapPlot", "LinePlot", "LineTrack", "ScatterPlot", "StackedLinePlot", "StackedLineTrack".
`chr`	The chromosome to filter on, e.g., chr="chr11".
`start`	The start location, e.g., start=110800000.
`end`	The end location, e.g., end=130383180.
`settings`	List of settings, e.g., list(title="Blocks Chart").
`colors`	List of colors. When chart is rendered to html this will be converted to a string encoded as JSON
`...`	Additional arguments passed to `epivizrData::register`, e.g., `type="bp"`, `columns=c("normal, cancer")`.

Value

An object of class EpivizChart.

Examples

data(tcga_colon_blocks)
start <- 99800000
end <- 103383180
blocks_track <- epivizChart(tcga_colon_blocks, chr="chr11", start=start, end=end)
# See package vignette for more examples.

data(tcga_colon_blocks)
start <- 99800000
end <- 103383180
blocks_track <- epivizChart(tcga_colon_blocks, chr="chr11", start=start, end=end)
# See package vignette for more examples.

Data container for an Epiviz chart component.

Description

Data container for an Epiviz chart component.

Fields

data: (list) Values of an epiviz chart's data attribute.
colors: (character) Epiviz chart's colors attribute.
settings: (list) Epiviz chart's settings attribute.
parent: An object of class EpivizEnvironment where chart is appended.

Methods

get_attributes()

Get attributes for rendering chart

get_available_settings()

Get available settings

get_colors()

Get chart colors

get_data()

Get chart data

get_parent()

Get parent

get_settings()

Get chart settings

navigate(chr, start, end)

Navigate chart to a genomic location

chr: Chromosome
start: Start location
end: End location

render_component(shiny = FALSE)

Render to html

revisualize(chart_type)

Revisualize chart as the given chart type

chart_type: The type of chart to be visualized (BlocksTrack, HeatmapPlot, LinePlot, LineTrack, ScatterPlot, StackedLinePlot, StackedLineTrack)

set_colors(colors)

Set chart colors

set_data(data)

Set chart data

set_settings(settings)

Modify current settings

settings: List of new settings. Call get_available_settings for settings available to modify.

Class providing data manager for epiviz charts.

Description

Class providing data manager for epiviz charts.

Fields

.ms_list: (environment) List of measurment records
.ms_idCounter: (integer) Counter for ID generator

Methods

add_genome(genome)

Add genome to data manager (for seqInfo)

chr: Chromosome
start: Start location
end: End location

add_measurements( obj, datasource_name = NULL, datasource_obj_name = deparse(substitute(obj)), ... )

get_data(measurements, chr = NULL, start = NULL, end = NULL)

Get data from data mgr based on measurements, chr, start, and end

measurements: List of EpivizMeasurements
chr: Chromosome
start: Start location
end: End location

register_shiny_handler(session)

Handlers to enable interactions with Shiny session.

session: Shiny session object

rm_all_measurements()

Remove all registered measurements

rm_measurements(ms_obj_or_id)

Remove registered measurements from a given data object

Data container for an Epiviz Data Source component.

Description

Data container for an Epiviz Data Source component.

Fields

provider_type: (character)
provider_id: (character)
provider_url: (character)

Methods

get_attributes(): Get attributes for rendering web component
get_component_type(): Get component type for prefix of random id generator
get_name(): Get name of Epiviz Web Component
get_provider_id(): Get provider id
get_provider_type(): Get provider type
get_provider_url(): Get provider url
render_component(shiny = FALSE): Render to html
set_provder_url(url): Set provider url
set_provider_id(id): Set provider id
set_provider_type(type): Set provider type

Initialize an `EpivizEnvironment` object.

Description

Initialize an EpivizEnvironment object.

Usage

epivizEnv(chr = NULL, start = NULL, end = NULL, interactive = FALSE, ...)
epivizEnv(chr = NULL, start = NULL, end = NULL, interactive = FALSE, ...)

Arguments

`chr`	The chromosome to filter on, e.g., `chr="chr11"`
`start`	The start location, e.g., `start=99800000`.
`end`	The end location, e.g., `end=130383180`.
`interactive`	(logical) enable if running a websocket/shiny server
`...`	Additional params to pass to `EpivizWebComponent`

Value

An object of class EpivizEnvironment

Examples

epiviz <- epivizEnv(chr="chr11", start=99800000, end=103383180)

epiviz <- epivizEnv(chr="chr11", start=99800000, end=103383180)

Data container for an Epiviz environment component.

Description

Data container for an Epiviz environment component.

Fields

charts: List of class EpivizViewComponent used to track nested elements.
interactive: Logical value of whether componenet is interactive with data source componenet..
epiviz_ds: EpivizDataSource object for interactive documents.

Methods

add_data(...)

Add data to environment's data manager

...: Arguments for add_measurements and register, e.g., data, datasource_name, datasource_obj_name, type, etc

add_genome(genome, type = "gene_info", datasource_name = NULL)

Add a genome to the view, and a genes-track.

genome: annotation object. eg. Homo.sapiens

append_chart(chart)

Append chart or navigation to environment

append_region(chr = NULL, start = NULL, end = NULL, ...)

Add a child Navigation element to the given genomic region

get_charts()

Get charts within environment

get_component_type()

Get component type for prefix of random id generator

get_measurements()

Get measurements

get_name()

Get name of Epiviz Web Component

get_rows(...)

Get row data from environment's data manager

get_values(...)

Get value data from environment's data manager

init_region(chr = NULL, start = NULL, end = NULL)

Initialize navigation based on a genomic region

chr: Chromosome
start: Start location
end: End location

init_regions(regions)

Initialize navigations based on genomic regions

regions: List of named lists of genomic locations, e.g., list(list(chr='chr11', start=99800000, end=103383180))

is_interactive()

Return whether the environment is interactive with a data source

navigate(chr = NULL, start = NULL, end = NULL)

Navigate environment to genomic location

chr: Chromosome
start: Start location
end: End location

order_charts(ordered_charts)

Order the charts within an environment

charts: An ordered list of EpivizViewComponent objects

plot(...)

Plot an EpivizChart within the environment

...: Arguments for epivizChart

register_shiny_handler(session)

Enable components to interact with Shiny session.

session: Shiny session object

remove_all_charts()

Remove all charts from environment

remove_chart(chart)

Remove chart from environment

render_component(shiny = FALSE)

Render to html

shiny: if rendering component in a shiny environment

set_charts(charts)

epivizNav(
  chr = NULL,
  start = NULL,
  end = NULL,
  parent = NULL,
  interactive = FALSE,
  ...
)
epivizNav(
  chr = NULL,
  start = NULL,
  end = NULL,
  parent = NULL,
  interactive = FALSE,
  ...
)

Arguments

`chr`	The chromosome to filter on, e.g., chr="chr11".
`start`	The start location, e.g., start=99800000.
`end`	The end location, e.g., end=130383180.
`parent`	An object of class `⁠[EpivizEnvironment⁠`] or `EpivizNavigation` to append the chart within.
`interactive`	(logical) enable if running a websocket/shiny server
`...`	Additional arguments for initializing navigation, e.g., gene and geneInRange.

Value

An object of class EpivizNavigation.

Examples

epiviz <- epivizNav(chr="chr11", start=99800000, end=103383180)

epiviz <- epivizNav(chr="chr11", start=99800000, end=103383180)

Data container for an Epiviz navigation component.

Description

Data container for an Epiviz navigation component.

Fields

gene: (character) Gene
geneInRange: (character) Nearest Gene in range.
parent: An object of class EpivizEnvironment where navigation is appended.

Methods

add_genome(genome, type = "gene_info", datasource_name = NULL)

Add a genome to the view, and a genes-track.

genome: annotation object. eg. Homo.sapiens

clone_charts(charts)

Clone EpivizCharts and append to navigation. Each chart must already exist in the navigation's data manager, otherwise an error will occur when attempting to intialize using their measurements

charts: list of EpivizCharts whose data exists in the navigation's data manager

get_attributes()

Get attributes for rendering chart

get_component_type()

Get component type for prefix of random id generator

get_gene()

Get gene

get_geneInRange()

Get gene in range

get_name()

Get name of Epiviz Web Component

render_component(shiny = FALSE)

Render to html

shiny: if rendering component in a shiny environment

set_gene(gene)

Set gene

set_geneInRange(gene)

chr: (CharacterOrNULL) Chromosome location.
start: (NumericOrNULL) Start location.
end: (NumericOrNULL) End location.
measurements: (ListOrNULL) list of measurements of class EpivizMeasurement.

Methods

get_attributes(): Get attributes for rendering web component
get_chr(): Get chromosome
get_end(): Get end
get_measurements(): Get measurements
get_start(): Get start
set_chr(chr): Set the chromosome
set_end(end): Set end
set_measurements(ms): Set measurements
set_start(start): Set start

Data container for an Epiviz Web component.

Description

Data container for an Epiviz Web component.

Fields

data_mgr: EpivizChartDataMgr
name: (character) Epiviz chart type (tag name).
class: (CharacterOrNULL) Epiviz chart's class attribute.
id: (character) Epiviz chart's id attribute.

Methods

get_attributes(): Get attributes for rendering web component
get_class(): Get class
get_data_mgr(): Get data manager
get_id(): Get id
get_name(): Get name of Epiviz Web Component
set_class(class): Set chart class
set_id(id): Set chart id
set_name(name): Set name

Construct URL for Websocket connection between R and UI

Description

Construct URL for Websocket connection between R and UI

Usage

get_available_chart_types()
get_available_chart_types()

Value

url

Construct URL for Websocket connection between R and UI

Description

Construct URL for Websocket connection between R and UI

Usage

get_registered_data_types()
get_registered_data_types()

Value

url

Method to add Heatmap Plot

Description

Method to add Heatmap Plot

Usage

HeatmapPlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
HeatmapPlot(x, y, ...)
HeatmapPlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
HeatmapPlot(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

JSON parser used by this package

Description

Currently this just renames fromJSON in the rjson package.

Usage

json_parser(
  json_str,
  file,
  method = "C",
  unexpected.escape = "error",
  simplify = TRUE
)
json_parser(
  json_str,
  file,
  method = "C",
  unexpected.escape = "error",
  simplify = TRUE
)

Arguments

`json_str`	json string to parse
`file`	file to read json_Str from
`method`	method used to parse json
`unexpected.escape`	handling escape characters, one of error, skip, keep
`simplify`	if TRUE, convert json-encoded lists to vectors

Value

a JSON object

Examples

json_parser('{"a":true, "b":false, "c":null}')
json_parser('{"a":true, "b":false, "c":null}')

JSON writer used by this package

Description

Currently this just renames toJSON in the rjson package.

Usage

json_writer(x, indent = 0, method = "C")
json_writer(x, indent = 0, method = "C")

Arguments

`x`	object to write to json
`indent`	integer specifying how much indentation to use when formatting the JSON object; if 0, no pretty-formatting is used
`method`	method used to write json

Value

a string with JSON encoding of object

Examples

json_writer(1:10)
json_writer(1:10)

Method to add Line Plot

Description

Method to add Line Plot

Usage

LinePlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
LinePlot(x, y, ...)
LinePlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
LinePlot(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Method to add Line Track

Description

Method to add Line Track

Usage

LineTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
LineTrack(x, y, ...)
LineTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
LineTrack(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Generic methods to plot charts and add navigation regions

Description

Generic methods to plot charts and add navigation regions

Usage

## S4 method for signature 'EpivizEnvironment,ANY'
plot(x, y, ...)
## S4 method for signature 'EpivizEnvironment,ANY'
plot(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Examples

## Not run: 
library(epivizrChart)
library(Homo.sapiens)
require(magrittr)

# example data set
data(sumexp)
# create an environment element
epivizEnv <- epivizEnv()

# chain and add navigation regions and plots.
epivizEnv %>% 
plot(sumexp, datasource_name="sumExp", columns=c("cancer", "normal")) %>% 
append_region(chr="chr11", start=118000000, end=121000000) %>% 
plot(sumexp, datasource_name="sumExp", columns=c("normal", "cancer"))
epivizEnv

## End(Not run)
## Not run: 
library(epivizrChart)
library(Homo.sapiens)
require(magrittr)

# example data set
data(sumexp)
# create an environment element
epivizEnv <- epivizEnv()

# chain and add navigation regions and plots.
epivizEnv %>% 
plot(sumexp, datasource_name="sumExp", columns=c("cancer", "normal")) %>% 
append_region(chr="chr11", start=118000000, end=121000000) %>% 
plot(sumexp, datasource_name="sumExp", columns=c("normal", "cancer"))
epivizEnv

## End(Not run)

Random ID generator for epiviz charts

Description

Random ID generator for epiviz charts

Usage

rand_id(prefix = "")
rand_id(prefix = "")

Arguments

prefix

prefix for random ID

Value

random ID

Method to add Scatter Plot

Description

Method to add Scatter Plot

Usage

ScatterPlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
ScatterPlot(x, y, ...)
ScatterPlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
ScatterPlot(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Method to add Stacked Blocks Track

Description

Method to add Stacked Blocks Track

Usage

StackedBlocksTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
StackedBlocksTrack(x, y, ...)
StackedBlocksTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
StackedBlocksTrack(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Method to add Stacked Line Plot

Description

Method to add Stacked Line Plot

Usage

StackedLinePlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
StackedLinePlot(x, y, ...)
StackedLinePlot(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
StackedLinePlot(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Method to add Stacked Line Track

Description

Method to add Stacked Line Track

Usage

StackedLineTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
StackedLineTrack(x, y, ...)
StackedLineTrack(x, y, ...)

## S4 method for signature 'EpivizEnvironment'
StackedLineTrack(x, y, ...)

Arguments

`x`	an object of type `EpivizEnvironment` or `EpivizNavigation`
`y`	a genomic data object
`...`	other parameters for the plot method

Example SummarizedExperiment for epivizr vignette

Description

Example SummarizedExperiment for epivizr vignette

Usage

data(sumexp)
data(sumexp)

Format

A SummarizedExperiment::RangedSummarizedExperiment object.

Example methylation data (blocks) for epivizr vignette.

Description

Example results from methylation analysis of human chromosome 11 using the minfi package of TCGA 450k beadarray samples. This object contains large regions of methylation difference between tumor and normal samples obtained from minfi::blockFinder().

Usage

data(tcga_colon_blocks)
data(tcga_colon_blocks)

Format

A GenomicRanges::GRanges object with 129 and mcols:

value: average smooth methylation difference within block
area: block area estimate (abs(value) * length)
cluster: id of cluster blockgroup within which block occurs
indexStart: index of first cluster in block
indexEnd: index of last cluster in block
L: number of clusters in block
clusterL: number of probes in block
p.value: permutation p.value based on difference conditioned on length
fwer: family-wise error rate estimate based on difference conditioned on length
p.valueArea: permutation p.value based on area
fwerArea: family-wise error rate estimate based on area

Source

TCGA project: https://tcga-data.nci.nih.gov/tcga/

Example methylation data (smoothed methylation levels) for epivizr vignette

Description

Example results from methylation analysis of human chromosome 11 using the minfi package of TCGA 450k beadarray samples. This object contains probe cluster level methylation estimates from minfi::blockFinder().

Usage

data(tcga_colon_curves)
data(tcga_colon_curves)

Format

A GenomicRanges::GRanges object with 7135 ranges and mcols:

id: probe cluster id
type: probe cluster type
blockgroup: probe cluster block group
diff: raw methylation percentage difference between normal and tumor
smooth: smooth methylation percentage difference between normal and tumor
normalMean: mean methylation estimate for normal samples
cancerMean: mean methylation estimate for cancer samples

Source

TCGA project: https://tcga-data.nci.nih.gov/tcga/

Example exon-level RNAseq data from TCGA project for epivizr vignette.

Description

A SummarizedExperiment::RangedSummarizedExperiment object containing exon-level counts from RNAseq data for colon tumor and normal tissue from the TCGA project. Only exons in human chromosome 11 are included.

Usage

data(tcga_colon_expression)
data(tcga_colon_expression)

Format

A SummarizedExperiment::RangedSummarizedExperiment object with 12,800 rows (exons) and 40 samples.

assay(tcga_colon_expression): exon-level count matrix
colData(tcga_colon_expression): a DataFrame containing sample information. Normal/Tumor status is given in column sample_type

Source

TCGA project: https://tcga-data.nci.nih.gov/tcga/

Package 'epivizrChart'

Help Index

Construct URL for Websocket connection between R and UI

Description

Usage

Arguments

Value

Initialize Epiviz Chart based on chart type

Description

Usage

Arguments

(taken from epivizr) register epiviz actions

Description

Usage

Arguments

(taken from epivizr) print settings in a readable format

Description

Usage

Arguments

Value

Generic method to add navigation regions

Description

Usage

Arguments

Example expression data from the Gene Expression barcode project

Description

Usage

Format

Method to add Blocks Track

Description

Usage

Arguments

Locations of CpG Islands

Description

Usage

Format

Get default chart settings and colors

Description

Usage

Arguments

Value

Data container for an Epiviz Blocks Track.

Description

Methods

Initialize an EpivizChart object to visualize in viewer or knit to HTML.

Description

Usage

Arguments

Value

Examples

Data container for an Epiviz chart component.

Description

Fields

Methods

Class providing data manager for epiviz charts.

Description

Fields

Methods

Data container for an Epiviz Data Source component.

Description

Fields

Methods

Initialize an EpivizEnvironment object.

Description

Usage

Arguments

Value

Examples

Data container for an Epiviz environment component.

Description

Fields

Methods

Data container for an Epiviz Genes Track.

Description

Methods

Data container for an Epiviz Heatmap Plot.

Description

Methods

Data container for an Epiviz Genes Track.

Description

Initialize an `EpivizChart` object to visualize in viewer or knit to HTML.

Initialize an `EpivizEnvironment` object.

Initialize an `EpivizNavigation` object to visualize in viewer or knit to HTML.