MakePhenotypingDotPlot

Creates a DotPlot using custom gene sets and attempts to coarsely group gene sets by cell type.

Usage

MakePhenotypingDotPlot(
  seuratObj,
  yField = "ClusterNames_0.2",
  scaled = T,
  gene_lists = c("Cytotoxicity", "EffectorCytokines"),
  assay = "RNA",
  scale.by = "size"
)

Arguments

seuratObj

A Seurat Object storing the count matrix to be used for phenotyping.

yField

The grouping variable used to calculate the average expression of genes and the y axis of the DotPlot.

scaled

A boolean defining whether to color dots by scaled expression or unscaled expression.

gene_lists

A vector of gene lists (defined by .RegisterGeneSet) to be queried and their genes be plotted.

assay

Which assay to use in the input seuratObj

scale.by

Allow different scaling methods for dot size. 'radius' will de-emphasize lower/intermediately percent expressed genes.