iSEE: iSEE: interactive SummarizedExperiment/SingleCellExperiment...

Description Usage Arguments Details Value Examples

View source: R/iSEE-main.R

Description

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

Usage

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iSEE(se, redDimArgs = NULL, colDataArgs = NULL, featAssayArgs = NULL,
  rowStatArgs = NULL, rowDataArgs = NULL, sampAssayArgs = NULL,
  colStatArgs = NULL, customDataArgs = NULL, customStatArgs = NULL,
  heatMapArgs = NULL, redDimMax = 5, colDataMax = 5,
  featAssayMax = 5, rowStatMax = 5, rowDataMax = 5,
  sampAssayMax = 5, colStatMax = 5, customDataMax = 5,
  customStatMax = 5, heatMapMax = 5, initialPanels = NULL,
  annotFun = NULL, customDataFun = NULL, customStatFun = NULL,
  colormap = ExperimentColorMap(), tour = NULL, appTitle = NULL,
  runLocal = TRUE, voice = FALSE)

Arguments

se

An object that is coercible to SingleCellExperiment.

redDimArgs

A DataFrame similar to that produced by redDimPlotDefaults, specifying initial parameters for the reduced dimension plots.

colDataArgs

A DataFrame similar to that produced by colDataPlotDefaults, specifying initial parameters for the column data plots.

featAssayArgs

A DataFrame similar to that produced by featAssayPlotDefaults, specifying initial parameters for the feature assay plots.

rowStatArgs

A DataFrame similar to that produced by rowStatTableDefaults, specifying initial parameters for the row statistics tables.

rowDataArgs

A DataFrame similar to that produced by rowDataPlotDefaults, specifying initial parameters for the row data plots.

sampAssayArgs

A DataFrame similar to that produced by sampAssayPlotDefaults, specifying initial parameters for the sample assay plots.

colStatArgs

A DataFrame similar to that produced by colStatTableDefaults, specifying initial parameters for the sample assay plots.

customDataArgs

A DataFrame similar to that produced by customDataPlotDefaults, specifying initial parameters for the custom data plots.

customStatArgs

A DataFrame similar to that produced by customStatTableDefaults, specifying initial parameters for the custom statistics tables.

heatMapArgs

A DataFrame similar to that produced by heatMapPlotDefaults, specifying initial parameters for the heatmaps.

redDimMax

An integer scalar specifying the maximum number of reduced dimension plots in the interface.

colDataMax

An integer scalar specifying the maximum number of column data plots in the interface.

featAssayMax

An integer scalar specifying the maximum number of feature assay plots in the interface.

rowStatMax

An integer scalar specifying the maximum number of row statistics tables in the interface.

rowDataMax

An integer scalar specifying the maximum number of row data plots in the interface.

sampAssayMax

An integer scalar specifying the maximum number of sample assay plots in the interface.

colStatMax

An integer scalar specifying the maximum number of column statistics tables in the interface.

customDataMax

An integer scalar specifying the maximum number of custom data plots in the interface.

customStatMax

An integer scalar specifying the maximum number of custom statistics tables in the interface.

heatMapMax

An integer scalar specifying the maximum number of heatmaps in the interface.

initialPanels

A DataFrame specifying which panels should be created at initialization. This should contain a Name character field and may have optional Width and Height integer fields, see Details.

annotFun

A function, similar to those returned by annotateEntrez or annotateEnsembl. The function should accept two parameters, se and row_index, and return a HTML element with annotation for the selected row.

customDataFun

A named list of functions for reporting coordinates to use in a custom data plot.

customStatFun

A named list of functions for reporting coordinates to use in a custom statistics table.

colormap

An ExperimentColorMap object that defines custom colormaps to apply to individual assays, colData and rowData covariates.

tour

A data.frame with the content of the interactive tour to be displayed after starting up the app.

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.

Details

Users can pass default parameters via DataFrame objects in redDimArgs and featAssayArgs. Each object can contain some or all of the expected fields (see redDimPlotDefaults). Any missing fields will be filled in with the defaults.

The number of maximum plots for each type of plot is set to the larger of *Max and nrow(*Args). Users can specify any number of maximum plots, though increasing the number will increase the time required to render the interface.

The initialPanels argument specifies the panels to be created upon initializing the interface. This should be a DataFrame containing a Name field specifying the identity of the panel, e.g., "Reduced dimension plot 1", "Row statistics table 2". Please refer to availablePanelTypes for the full list of panels available. The trailing number should not be greater than the number of maximum plots of that type. Users can also define the Width field, specifying the width of each panel from 2 to 12 (values will be coerced inside this range); and the Height field, specifying the height of each panel from 400 to 1000 pixels. By default, one panel of each type (where possible) will be generated, with height of 500 and width of 4.

The tour argument needs to be provided in a form compatible with the format expected by the rintrojs package. There should be two columns, element and intro, with the former describing the element to highlight and the latter providing some descriptive text. See https://github.com/carlganz/rintrojs#usage for more information.

By default, categorical data types such as factor and character are limited to 24 levels, beyond which they are coerced to numeric variables for faster plotting. This limit may be set to a different value as a global option, e.g. options(iSEE.maxlevels=30).

Value

A Shiny app object is returned, for interactive data exploration of the SummarizedExperiment or SingleCellExperiment object.

Examples

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library(scRNAseq)
data(allen)
class(allen)

# Example data ----

library(scater)
sce <- as(allen, "SingleCellExperiment")
counts(sce) <- assay(sce, "tophat_counts")
sce <- normalize(sce)

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

# launch the app itself ----

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

csoneson/iSEE documentation built on Dec. 13, 2018, 4:12 p.m.