modeGating {iSEE} | R Documentation |
App pre-configured to link multiple feature assay plots
modeGating(se, features, featAssayMax = max(2, nrow(features)), ..., plot_width = 4)
se |
An object that coercible to SingleCellExperiment |
features |
|
featAssayMax |
Maximal number of feature assay plots in the app. |
... |
Additional arguments passed to |
plot_width |
The grid width of linked plots (numeric vector of
length either 1 or equal to |
A Shiny App preconfigured with multiple chain-linked feature
expression plots is launched for interactive data exploration of the
SingleCellExperiment
/ SummarizedExperiment
object
library(scRNAseq) data(allen) class(allen) # Example data ---- library(scater) sce <- as(allen, "SingleCellExperiment") counts(sce) <- assay(sce, "tophat_counts") sce <- normalize(sce) # Select top variable genes ---- plot_count <- 6 rv <- rowVars(logcounts(sce)) 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, featAssayMax = 6) if (interactive()) { shiny::runApp(app, port = 1234) }