plotMetadataCorHeatmap: Plot Metadata Correlation Heatmap

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

Plot Metadata Correlation Heatmap

Description

This function plots a heatmap of metadata correlation values. It accepts a Seurat object and a set of metadata columns to correlate. The correlations are calculated using either Pearson or Spearman methods, and the resulting heatmap can include the principal component (PCA) values and be saved with a specific suffix.

Usage

plotMetadataCorHeatmap(
  columns = c("nCount_RNA", "nFeature_RNA", "percent.mito", "percent.ribo"),
  obj,
  cormethod = c("pearson", "spearman")[1],
  main = paste("Metadata", cormethod, "correlations"),
  show_numbers = FALSE,
  digits = 1,
  suffix = NULL,
  add_PCA = TRUE,
  n_PCs = 8,
  w = ceiling((length(columns) + n_PCs)/2),
  h = w,
  use_ggcorrplot = FALSE,
  n_cutree = (n_PCs),
  ...
)

Arguments

columns	A vector of metadata column names to calculate correlations. Default: c("nCount_RNA", "nFeature_RNA", "percent.mito", "percent.ribo").
obj	The main Seurat object used for calculations. No default value.
cormethod	The method to calculate correlations. Can be either "pearson" or "spearman". Default: "pearson".
main	The main title for the plot. Default: "Metadata correlations" followed by the correlation method.
show_numbers	Logical, determines if correlation values should be displayed on the plot. Default: FALSE.
digits	The number of decimal places for displayed correlation values. Default: 1.
suffix	A suffix added to the output filename. Default: NULL.
add_PCA	Logical, determines if PCA values should be included in the correlation calculation. Default: TRUE.
n_PCs	The number of PCA components to be included if 'add_PCA' is TRUE. Default: 8.
w	The width of the plot in inches. Default: ceiling((length(columns)+n_PCs)/2).
h	The height of the plot in inches. Default: the value of w.
use_ggcorrplot	Logical, determines if the ggcorrplot package should be used for plotting. Default: FALSE.
n_cutree	The number of clusters to be used in hierarchical clustering. Default: the number of PCs.
...	Additional parameters passed to the internally called ggcorrplot function.

See Also

ggcorrplot

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