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

Usage

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

Arguments

seuratObjHD: 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".

Value

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