plotDecontXContamination: Plots contamination on UMAP coordinates

In campbio/celda: CEllular Latent Dirichlet Allocation

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.

campbio/celda documentation built on April 5, 2024, 11:47 a.m.