SCENIC (version 1.1.2-01)

plotTsne_rgb: plotTsne_rgb

Description

Colors the t-SNE based on the activity of 3 (groups of) regulons

Usage

plotTsne_rgb(scenicOptions, regulonNames, aucType = "AUC",
  aucMaxContrast = 0.8, offColor = "#c0c0c030", showPlot = TRUE,
  tSNE_fileName = NULL, ...)

Arguments

scenicOptions

Fields used: AUC matrix (continuous or binary), default t-SNE.

regulonNames

Regulons 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 t-SNE.

tSNE_fileName

tSNE file name. If null, the default t-SNE is used.

...

Other arguments to pass to the plot function.

Value

The cell colors (invisible)

Examples

# NOT RUN {
par(mfrow=c(1,2))

regulonNames <- c("Dlx1", "Sox8")
cellCol <- plotTsne_rgb(scenicOptions, regulonNames, aucType="AUC", aucMaxContrast=0.6)
text(-5,-23, attr(cellCol,"red"), col="red", cex=.7)
text(-10,-18, attr(cellCol,"green"), col="green", cex=.7)

regulonNames <- list(red=c("Dlx1","Dlx5"),
                     green=c("Neurod1"),
                     blue=c("Sox8"))
cellCol <- plotTsne_rgb(scenicOptions, regulonNames, aucType="Binary")

# }