iSEE {iSEE}R Documentation

iSEE: interactive SummarizedExperiment/SingleCellExperiment Explorer

Description

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

Usage

iSEE(se, redDimArgs = NULL, colDataArgs = NULL, featAssayArgs = NULL,
  rowStatArgs = NULL, rowDataArgs = NULL, heatMapArgs = NULL,
  redDimMax = 5, colDataMax = 5, featAssayMax = 5, rowStatMax = 5,
  rowDataMax = 5, heatMapMax = 5, initialPanels = NULL, annotFun = NULL,
  colormap = ExperimentColorMap(), tour = NULL, appTitle = NULL,
  runLocal = TRUE)

Arguments

se

An object that is coercible to SingleCellExperiment.

redDimArgs

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

colDataArgs

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

featAssayArgs

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

rowStatArgs

A DataFrame similar to that produced by rowStatTableDefaults, specifying initial parameters for the plots.

rowDataArgs

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

heatMapArgs

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

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.

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, constructed in the form of annotateEntrez or annotateEnsembl. This function is built in a way to generate itself a function supposed to accept two parameters, se and row_index, to have a unified yet flexible interface to generate additional information to display for the selected genes of interest.

colormap

An ExperimentColorMap object that defines custom color maps 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. Defaults to NULL. More information is provided in the details.

appTitle

A string indicating the title to be displayed in the app. If not provided, the app displays the version info of iSEE. Users can specify this to provide a compact description of the dataset, or the PubMedID for the input data.

runLocal

A logical indicating whether the app is to be run locally or remotely on a server, which determines how documentation will be accessed.

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". 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, where the variables element and intro have to be present. See more information at https://github.com/carlganz/rintrojs#usage regarding the values that the element can assume for proper displaying.

Value

A Shiny App is launched for interactive data exploration of the SummarizedExperiment/SingleCellExperiment object

Examples

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)
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)
}

[Package iSEE version 1.0.1 Index]