iSEE (version 0.98.2)

iSEE: iSEE: interactive SingleCell/Summarized Experiment Explorer

Description

Interactive visualization of single-cell data using a Shiny interface.

Usage

iSEE(se, redDimArgs = NULL, colDataArgs = NULL, geneExprArgs = NULL,
  geneStatArgs = NULL, redDimMax = 5, colDataMax = 5, geneExprMax = 5,
  geneStatMax = 5, initialPanels = NULL, annot.orgdb = NULL,
  annot.keytype = "ENTREZID", annot.keyfield = NULL,
  colormap = ExperimentColorMap(), run_local = TRUE)

Arguments

se

An object that 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.

geneExprArgs

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

geneStatArgs

A DataFrame similar to that produced by geneStatTableDefaults, 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.

geneExprMax

An integer scalar specifying the maximum number of gene expression plots in the interface.

geneStatMax

An integer scalar specifying the maximum number of gene statistic tables in the interface.

initialPanels

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

annot.orgdb

An org.*.db annotation object from which Entrez identifiers can be retrieved.

annot.keytype

A string specifying the keytype to use to query annot.orgdb.

annot.keyfield

A string specifying the field of rowData(se) containing the keys of type annot.keytype. If NULL, the row names of se are used as the keys.

colormap

An '>ExperimentColorMap object that defines custom color maps to apply to individual assays, colData, and rowData covariates.

run_local

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

Value

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

Details

Users can pass default parameters via DataFrame objects in redDimArgs and geneExprArgs. 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", "Gene statistics table 2". The trailing number should not be greater than the number of maximum plots of that type. The Width field may also be specified describing the width of the panel from 2 to 12 (values will be coerced inside this range).

If annot.orgdb is specified, gene information will be retrieved upon selection of particular genes in the data table. No retrieval is performed if annot.orgdb=NULL.

Examples

# NOT RUN {
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)
sce

# launch the app itself ----

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