plot.Gene.Cor.Heatmap: Plot Gene Correlation Heatmap

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Plot Gene Correlation Heatmap

Description

Generates a heatmap visualization of gene correlations based on expression data. Useful for identifying groups of genes that exhibit similar expression patterns across different conditions or cell types in a Seurat object.

Usage

## S3 method for class 'Gene.Cor.Heatmap'
plot(
  genes,
  assay.use = "RNA",
  slot.use = c("data", "scale.data", "data.imputed")[1],
  quantileX = 0.95,
  min.g.cor = 0.3,
  calc.COR = FALSE,
  cutRows = NULL,
  cutCols = cutRows,
  obj = combined.obj,
  ...
)

Arguments

genes	Vector of gene symbols to include in the correlation analysis and heatmap.
assay.use	Assay from which to retrieve expression data within the Seurat object. Default: 'RNA'.
slot.use	Specifies which slot of the assay to use for expression data ⁠('data', 'scale.data', 'data.imputed')⁠; Default: first item ('data').
quantileX	Quantile level for calculating expression thresholds. Default: 0.95.
min.g.cor	Minimum absolute gene correlation value for inclusion in the heatmap. Default: 0.3.
calc.COR	Logical flag to calculate correlation matrix if not found in ⁠@misc⁠. Default: FALSE.
cutRows	Height at which to cut the dendrogram for rows, determining cluster formation. Default: NULL.
cutCols	Height at which to cut the dendrogram for columns, determining cluster formation. Default: same as cutRows.
obj	Seurat object containing the data. Default: combined.obj.
...	Additional parameters passed to the internally called functions.

Examples

## Not run: 
if (interactive()) {
  plot.Gene.Cor.Heatmap(genes = c("Gene1", "Gene2", "Gene3"), obj = combined.obj)
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.