dimUMAPPlot: dimUMAPPlot Function

In aifimmunology/PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

dimUMAPPlot Function

Description

This function allows to perform UMAP visualization of gene of interest list.

Usage

dimUMAPPlot(
  data_object,
  nPC = 30,
  gene_oi,
  group_column,
  plotname = NULL,
  repel = FALSE,
  filePATH = NULL,
  fileName = NULL
)

Arguments

data_object	Input PALMO S4 object. Contains annotation table and single cell data stored as Seurat scRNA object.
nPC	Number of PCAs to be used for UMAP, Default is 30
gene_oi	Genes of interest to explore, required
group_column	User-defined group name column from annotation table or Seurat annotation column. Example, group_column='celltype' (required)
plotname	User-defined output file name (required)
repel	UMAP plot with labels repel=TRUE. Default FALSE
filePATH	User-defined output directory PATH Default, current directory
fileName	User-defined file name, Default outputFile

Value

UMAP plot

Examples

## Not run: 
dimUMAPPlot(data_object=pamo_obj, nPC=15, gene_oi=stable_gene,
group_column='celltype', plotname='stable')

## End(Not run)

aifimmunology/PALMO documentation built on Oct. 21, 2022, 7:39 p.m.