PALMO (version 0.1.2)

dimUMAPPlot: 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
)

Value

UMAP plot

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

Examples

if (FALSE) {
dimUMAPPlot(data_object=pamo_obj, nPC=15, gene_oi=stable_gene,
group_column='celltype', plotname='stable')
}