Plots contamination on UMAP coordinates

Source: R/plot_decontx.R

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

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.

See also

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

Author

Shiyi Yang, Joshua Campbell