modeReducedDim {iSEEu} | R Documentation |
This mode launches a Shiny App preconfigured with multiple linked reduced
dimension plots for interactive data exploration of the
SingleCellExperiment
object.
modeReducedDim( se, includeNames = reducedDimNames(se), colorBy = NULL, ..., plotWidth = NULL )
se |
An object that coercible to SingleCellExperiment |
includeNames |
Character vector with the names of reduced dimensions
to display as individual panels. The default uses all available in
|
colorBy |
Character scalar controlling coloring of cells. Must match either
to one of |
... |
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") sce <- runPCA(sce, ncomponents = 30) sce <- runTSNE(sce) sce <- runUMAP(sce) reducedDimNames(sce) # launch the app ---- # ... coloring by a column data variable app <- modeReducedDim(sce, colorBy = "Primary.Type") if (interactive()) { shiny::runApp(app, port=1234) } # ... coloring by a feature app <- modeReducedDim(sce, colorBy = "Scnn1a") if (interactive()) { shiny::runApp(app, port=1234) }