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

Arguments

object

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.

pt.size

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

point_size

Deprecated alias(es) for pt.size; supply exactly one of the two. It will be removed in scop 1.0.0.

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.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A named list of ggplot objects.