| 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)
}