plotEmb_rgb: plotEmb_rgb

In aertslab/AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

plotEmb_rgb

Description

Colors the embeddings (t-SNE/Umap) based on the activity of 3 (groups of) geneSets

Usage

plotEmb_rgb(
  aucMat,
  embedding,
  geneSetsByCol,
  aucType = "AUC",
  aucMaxContrast = 0.8,
  offColor = "#c0c0c030",
  showPlot = TRUE,
  showLegend = TRUE,
  ...
)

Arguments

aucMat	AUC matrix (continuous or binary)
embedding	AUC matrix (continuous or binary)
geneSetsByCol	Gene sets to plot
aucType	"AUC" or "Binary"
aucMaxContrast	To increase the AUC contrast decrease the value.
offColor	Color por the cells completelly off. To deactivate (color as black), set to NULL.
showPlot	Whether to plot the coloured embeddings.
showLegend	Whether to plot add a legend to the plot.
...	Other arguments to pass to the plot function.

Value

The cell colors (invisible)

aertslab/AUCell documentation built on March 12, 2024, 11:40 p.m.