Plot scPagwas Scores

Plot the score and adjusted p-value metadata produced by RunscPagwas() on an existing Seurat reduction. The plots are returned and can optionally be saved as PDF files.

Usage

PlotscPagwas(
  srt,
  reduction = c("umap", "tsne"),
  features = NULL,
  p_threshold = 0.05,
  output.dir = NULL,
  width = 7,
  height = 7,
  point_size = NULL,
  palette = "Spectral",
  palcolor = NULL,
  significance_palette = "Chinese",
  significance_palcolor = NULL,
  do_plot = TRUE
)

Arguments

srt

A Seurat object returned by RunscPagwas().

reduction

Reduction used for plotting, either "umap" or "tsne".

features

Numeric scPagwas metadata columns to plot. By default, available gPAS, TRS, and down-TRS score columns are used.

p_threshold

Adjusted p-value threshold used to identify significant cells. Set to NULL to omit the significance plot.

output.dir

Optional directory in which to save PDF files.

width, height

PDF dimensions in inches.

point_size

Point size passed to FeatureDimPlot() and CellDimPlot().

palette, palcolor

Palette used for continuous scPagwas scores, passed to FeatureDimPlot().

significance_palette, significance_palcolor

Palette used for the significance groups, passed to CellDimPlot().

do_plot

Whether to print each plot.

Value

A named list of ggplot objects.