Plot CNV Results into a Heatmap Builds a heatmap to visualize the CNV results based on genomic scores.

Usage

plotCNVResults(
  seuratObj,
  referenceVar = NULL,
  clustersVar = "cnv_clusters",
  splitPlotOnVar = clustersVar,
  denoise = TRUE,
  savePath = ".",
  printPlot = FALSE,
  referencePalette = "default",
  clusters_palette = "default",
  outputType = "png",
  raster_resize_mat = TRUE
)

Arguments

seuratObj: A Seurat object containing the genomic scores computed previously.
referenceVar: The name of the metadata column in the Seurat object containing reference annotations.
clustersVar: The name of the metadata column containing cluster information (default = "cnv_clusters").
splitPlotOnVar: The name of the metadata column used to split the heatmap rows (e.g., cell type or cluster) (default = clustersVar).
denoise: If TRUE, the denoised data will be used in the heatmap (default = TRUE).
savePath: The path where the heatmap will be saved. If NULL, the plot will not be saved (default = ".").
printPlot: Logical. If TRUE, prints the heatmap to the console.
referencePalette: A color palette for referenceVar. You can provide a custom palette as a vector of color codes (e.g., c("#FF0000", "#00FF00")).
clusters_palette: A color palette for clustersVar. You can provide a custom palette as a vector of color codes (e.g., c("#F8766D", "#A3A500", "#00BF7D")).
outputType: Character. Specifies the file format for saving the plot, either "png" or "pdf".
raster_resize_mat: Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image. Default is TRUE. If rendering fails with TRUE, the function automatically retries with FALSE.

Value

This function generates a heatmap and saves it as a .pdf or .png file in the specified path (default = working directory).