plotEmb_rgb: plotEmb_rgb

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

plotEmb_rgb

Description

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

Usage

plotEmb_rgb(
  object,
  regulonNames,
  aucType = "AUC",
  aucMaxContrast = 0.8,
  offColor = "#c0c0c030",
  showPlot = TRUE,
  showLegend = TRUE,
  tSNE_fileName = NULL,
  ...
)

## S4 method for signature 'list'
plotEmb_rgb(
  object,
  regulonNames,
  aucType = "AUC",
  aucMaxContrast = 0.8,
  offColor = "#c0c0c030",
  showPlot = TRUE,
  showLegend = TRUE,
  tSNE_fileName = NULL,
  ...
)

## S4 method for signature 'ScenicOptions'
plotEmb_rgb(
  object,
  regulonNames,
  aucType = "AUC",
  aucMaxContrast = 0.8,
  offColor = "#c0c0c030",
  showPlot = TRUE,
  showLegend = TRUE,
  tSNE_fileName = NULL,
  ...
)

Arguments

object	If 'scenicOptions' it will use the fields: AUC matrix (continuous or binary), and default t-SNE. If 'list', provide list(mat4col=.., emb=...)
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 embeddings.
showLegend	Whether to plot add a legend to the plot.
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

par(mfrow=c(1,2))

regulonNames <- c("Dlx1", "Sox8")
cellCol <- plotEmb_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 <- plotEmb_rgb(scenicOptions, regulonNames, aucType="Binary")

#OR if already loaded:
mat2col <- readRDS("int/2.2_motifs_AUC.Rds")
emb <- readRDS("int/tSNE_AUC_05pcs_05perpl.Rds")
cellCol <- plotEmb_rgb(list(mat2col=mat2col, emb=emb), regulonNames, aucType="Binary")

aertslab/SCENIC documentation built on April 7, 2024, 10 a.m.