plotEmb_rgb {AUCell} | R Documentation

## 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)

[Package AUCell version 1.14.0 Index]