PlotAverageAdtCounts: Plot Average ADT counts

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Plot Average ADT counts

Description

Creates a heatmap with average counts of each ADT markers based on one or more grouping fields

Usage

PlotAverageAdtCounts(
  seuratObj,
  groupFields = c("ClusterNames_0.2", "ClusterNames_0.4", "ClusterNames_0.6"),
  assayName = "ADT",
  layer = "counts",
  outFile = NA,
  normalization.method = "CLR",
  margin = 1
)

Arguments

seuratObj	The seurat object where data will be added.
groupFields	The directory holding raw count data, generally the raw_feature_bc_matrix from the cellranger outs folder
assayName	The name of the assay holding data
layer	The assay layer to use for average expression data
outFile	If provided, the heatmap will be written to this file
normalization.method	The normalization method to apply after AverageExpression(). If null, this will be skipped.
margin	This is provided to Seurat::NormalizeData()

bimberlabinternal/CellMembrane documentation built on Dec. 25, 2024, 8:10 a.m.