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Dimensional reduction plot with CHOIR clusters labeled

plotCHOIR.Rd

Generate a dimensionality reduction embedding plot colored according to the clusters identified by CHOIR. Additionally permits plotting mean prediction accuracy scores for pairs of clusters as an overlay.

Usage

plotCHOIR(
  object,
  key = "CHOIR",
  reduction = NULL,
  cells = NULL,
  legend = TRUE,
  accuracy_scores = FALSE,
  plot_nearest = TRUE,
  ...
)

Arguments

object

An object of class 'Seurat', 'SingleCellExperiment', or 'ArchRProject' that has undergone CHOIR clustering.

key

The name under which CHOIR-related data for this run is retrieved from the object. Defaults to 'CHOIR'.

reduction

A character vector indicating which CHOIR subtree dimensionality reduction to plot (e.g., 'P0_reduction_UMAP', 'P1_reduction_UMAP'). Default = NULL will plot the UMAP of the 'P0_reduction_UMAP' generated by CHOIR.

cells

Vector of cell names to plot. Default is all cells.

legend

A boolean value indicating whether to include a legend. Defaults to TRUE.

accuracy_scores

A boolean value indicating whether to overlay pairwise cluster comparison accuracy scores onto UMAP. Default = TRUE.

plot_nearest

A boolean value indicating whether to only plot the accuracy score for each cluster's nearest neighboring cluster. Only relevant if accuracy_scores is TRUE. Defaults to TRUE.

...

Extra parameters passed to Seurat::DimPlot()

Value

A ggplot object.