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

View source: R/Seurat.Utils.R

plot.Gene.Cor.HeatmapR Documentation

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.