plotDecontXContamination {celda} | R Documentation

## Plots contamination on UMAP coordinates

### Description

A scatter plot of the UMAP dimensions generated by DecontX with cells colored by the estimated percentation of contamation.

### Usage

    plotDecontXContamination(
      x,
      batch = NULL,
      colorScale = c("blue", "green", "yellow", "orange", "red"),
      size = 1
    )

### Arguments

`x` | Either a SingleCellExperiment with `decontX` results stored in `metadata(x)$decontX` or the result from running decontX on a count matrix.
`batch` | Character. Batch of cells to plot. If `NULL`, then the first batch in the list will be selected. Default `NULL`.
`colorScale` | Character vector. Contains the color spectrum to be passed to `scale_colour_gradientn` from package 'ggplot2'. Default c("blue","green","yellow","orange","red").
`size` | Numeric. Size of points in the scatterplot. Default 1.

### Value

Returns a `ggplot` object.

### Author(s)

Shiyi Yang, Joshua Campbell

### See Also

See `decontX` for a full example of how to estimate and plot contamination.

[Package celda version 1.8.1 Index]