modeGating {iSEEu} | R Documentation |
This mode launches a Shiny App preconfigured with multiple chain-linked
feature expression plots for interactive data exploration of the
SingleCellExperiment or
SummarizedExperiment
object.
modeGating(se, features, plotAssay = NA_character_, ..., plotWidth = 4)
se |
An object that coercible to SingleCellExperiment-class |
features |
|
plotAssay |
The assay (one of assayNames(se)) to use for the plots
(character vector of length either 1 or equal to |
... |
Additional arguments passed to |
plotWidth |
The grid width of linked plots (numeric vector of
length either 1 or equal to |
A Shiny app object is returned.
library(scRNAseq) # Example data ---- sce <- ReprocessedAllenData(assays="tophat_counts") class(sce) library(scater) sce <- logNormCounts(sce, exprs_values="tophat_counts") # Select top variable genes ---- plot_count <- 6 rv <- rowVars(assay(sce, "tophat_counts")) top_var <- head(order(rv, decreasing=TRUE), plot_count*2) top_var_genes <- rownames(sce)[top_var] plot_features <- data.frame( x=head(top_var_genes, plot_count), y=tail(top_var_genes, plot_count), stringsAsFactors=FALSE ) # launch the app itself ---- app <- modeGating(sce, features = plot_features) if (interactive()) { shiny::runApp(app, port=1234) }