fastCNV_10XHD calls all of the internal functions needed to compute the putative CNV on a Seurat Visium HD object or a list of Seurat Visium HD objects

This function orchestrates the CNV analysis on a Seurat Visium HD object (or multiple objects). It calls internal functions such as CNVAnalysis and PlotCNVResults to compute the CNVs and generate heatmaps. The results are saved in the metadata of the Seurat object(s), with options for generating and saving plots.

Usage

fastCNV_10XHD(
  seuratObjHD,
  sampleName,
  referenceVar = NULL,
  referenceLabel = NULL,
  assay = "Spatial.016um",
  pooledReference = TRUE,
  denoise = TRUE,
  scaleOnReferenceLabel = TRUE,
  thresholdPercentile = 0.01,
  geneMetadata = getGenes(),
  windowSize = 150,
  windowStep = 10,
  saveGenomicWindows = FALSE,
  topNGenes = 7000,
  chrArmsToForce = NULL,
  genesToForce = NULL,
  regionToForce = NULL,
  getCNVPerChromosomeArm = TRUE,
  getCNVClusters = FALSE,
  tumorLabel = NULL,
  k_clusters = NULL,
  h_clusters = NULL,
  plotDendrogram = FALSE,
  plotClustersOnDendrogram = FALSE,
  plotElbowPlot = FALSE,
  doPlot = TRUE,
  printPlot = FALSE,
  savePath = ".",
  outputType = "png",
  clustersVar = "cnv_clusters",
  splitPlotOnVar = clustersVar,
  referencePalette = "default"
)

Arguments

seuratObjHD: Seurat object or list of Seurat objects to perform the CNV analysis on.
sampleName: Name of the sample or a list of names corresponding to the samples in the seuratObj.
referenceVar: The variable name of the annotations in the Seurat metadata to be used as reference.
referenceLabel: The label given to the observations you want as reference (can be any type of annotation).
assay: Name of the assay to run the CNV on. Takes the results of prepareCountsForCNVAnalysis by default if available.
pooledReference: Default is TRUE. Will build a pooled reference across all samples if TRUE.
denoise: If TRUE, the data will be denoised (default = TRUE).
scaleOnReferenceLabel: If TRUE, scales the results depending on the normal observations (default = TRUE).
thresholdPercentile: Which quantiles to take (default 0.01). For example, 0.01 will take quantiles between 0.01-0.99. Background noise appears with higher numbers.
geneMetadata: List of genes and their metadata (default uses genes from Ensembl version 113).
windowSize: Size of the genomic windows for CNV analysis (default = 150).
windowStep: Step between the genomic windows (default = 10).
saveGenomicWindows: If TRUE, saves the information of the genomic windows in the current directory (default = FALSE).
topNGenes: Number of top expressed genes to keep (default = 7000).
chrArmsToForce: A chromosome arm (e.g., "8p", "3q") or a list of chromosome arms (e.g., c("3q", "8p", "17p")) to force into the analysis.
genesToForce: A list of genes to force into the analysis (e.g. c("FOXP3","MUC16","SAMD15")).
regionToForce: Chromosome region to force into the analysis (vector containing chr, start, end).
getCNVPerChromosomeArm: If TRUE, will save the CNV per chromosome arm into the metadata.
getCNVClusters: If TRUE, will perform clustering on the CNV scores and save them in the metadata of the Seurat object as cnv_clusters.
tumorLabel: The label within referenceVar that specifies the tumor/malignant population (can be any type of annotation).
k_clusters: Optional. Number of clusters to cut the dendrogram into. If NULL, the optimal number of clusters is determined automatically using the elbow method.
h_clusters: Optional. The height at which to cut the dendrogram for clustering. If both k and h are provided, k takes precedence.
plotDendrogram: Logical. Whether to plot the dendrogram (default = FALSE).
plotClustersOnDendrogram: Logical. Whether to highlight clusters on the dendrogram (default = FALSE).
plotElbowPlot: Logical. Whether to plot the elbow plot used for determining the optimal number of clusters (default = FALSE).
doPlot: If TRUE, will build a heatmap for each of the samples (default = TRUE).
printPlot: If TRUE, the heatmap will be printed in the console (default = FALSE, the plot will only be saved in a PDF).
savePath: Path to save the heatmap plot. If NULL, the plot won't be saved (default = .).
outputType: Specifies the file format for saving the plot, either "png" or "pdf" (default = "png").
clustersVar: The name of the metadata column containing cluster information (default = "cnv_clusters").
splitPlotOnVar: The name of the metadata column to split the observations during the plotCNVResults step, if different from referenceVar.
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")).

Value

A Seurat object or a list of Seurat objects after all the analysis is complete. Heatmaps of the CNVs for every object in seuratObj are generated and saved in the specified path (default = current working directory).