modeReducedDim: App pre-configured to compare multiple reduced dimension...
In iSEEu: iSEE Universe

Description Usage Arguments Value Examples

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 `reducedDimNames(se)`.
`colorBy`	Character scalar controlling coloring of cells. Must match either to one of `colnames(colData(se))` or `rownames(se)`. If coloring by a colData column, a column data plot is opened in addition to the reduced dimension panels. If coloring by a feature, a row statistics table is openend in addition to the reduced dimension panels, from which the latter are receiving the color.
`...`	Additional arguments passed to `iSEE`.
`plotWidth`	The grid width of linked plots (numeric vector of length either 1 or equal to `length(includeNames)`). The total width of the window is 12, so `plotWidth = 4` for example will show three panels per row. If `plotWidth = NULL` (the default), a value will be estimated depending on the number of reduced dimension panels.

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)
}