plotCNA_withAnnotCells: plotCNA_withAnnotCells allows generating a heatmap of the...

In AntonioDeFalco/SCEVAN: SCEVAN

plotCNA_withAnnotCells allows generating a heatmap of the copy number profile of each cell, adding cell annotations as tracks on the heatmap.

Description

plotCNA_withAnnotCells allows generating a heatmap of the copy number profile of each cell, adding cell annotations as tracks on the heatmap.

Usage

plotCNA_withAnnotCells(
  SampleName,
  metadata,
  COLUMNS_TO_PLOT,
  outputPATH = "./output/",
  SUBCLONE = FALSE,
  hcc = NULL,
  plotNAME = "heatmap_with_annotation.png",
  par_cores = 20
)

Arguments

SampleName	Sample name used in pipelineCNA
metadata	data.frame cells (rownames) and annotations (columns)
COLUMNS_TO_PLOT	columns of metadata to be added as tracks in the heatmap
outputPATH	output folder of pipelineCNA (optional)
SUBCLONE	Boolean value TRUE if you are interested in CNA matrix of sublclone and FALSE if you are interested in CNA matrix of all cells.
hcc	if you have previously computed clustering for the heatmap (optional - default 0.5)
plotNAME	name file to save the figure (optional)
par_cores	number of cores used for clustering (optional - default 20)

Examples

plotCNA_withAnnotCells(SampleName, metadata, c("CellType","Tissue","Cluster"))

AntonioDeFalco/SCEVAN documentation built on April 14, 2025, 6:33 a.m.