MakePhenotypingDotPlot: MakePhenotypingDotPlot

In bimberlabinternal/RIRA_classification: A package for the Rhesus Immune Reference Atlas (RIRA): A multi-tissue single-cell landscape of immune cells

MakePhenotypingDotPlot

Description

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.

bimberlabinternal/RIRA_classification documentation built on April 14, 2025, 5:59 p.m.