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

if (FALSE) { # \dontrun{
plotCNA_withAnnotCells(SampleName, metadata, c("CellType","Tissue","Cluster"))
} # }