heatmap_calc_clust_median: Calculate and plot heatmap of cluster medians

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

Calculate and plot heatmap of cluster medians

Description

This function calculates the median of specified variables in a dataframe, grouped by a column ('ident'). The function also provides an option to scale the medians, subset the ident levels, and either return a matrix of median values or plot a heatmap.

Usage

heatmap_calc_clust_median(
  meta,
  ident,
  subset_ident_levels = FALSE,
  variables,
  scale = TRUE,
  suffix = NULL,
  return_matrix = FALSE,
  plotname = "Median metadata values by cluster",
  n_cut_row = NA,
  n_cut_col = NA,
  w = ceiling(length(variables)/2),
  ...
)

Arguments

meta	A dataframe containing metadata from a Seurat object.
ident	A character string representing the column name to be used for grouping the data.
subset_ident_levels	An optional vector of ident levels to subset. Default is FALSE.
variables	A character vector containing the names of columns for which to calculate the median.
scale	A logical indicating whether to scale the medians. Default is TRUE.
suffix	A character string added to the plot file name if not returning a matrix. Default is NULL.
return_matrix	A logical indicating whether to return a matrix of medians, or plot a heatmap. Default is FALSE.
plotname	A character string representing the main title for the plot. Default is "Median metadata values by cluster".
n_cut_row	The number of row rows to cut the tree into on the pheatmap. Default is NA (none).
n_cut_col	The number of column clusters to cut the tree into on the pheatmap. Default is NA (none)
w	The width of the plot (if not returning a matrix). Default is half the number of variables.
...	Additional parameters passed to the pheatmap function.

Value

If 'return_matrix' is TRUE, a matrix where rows correspond to the unique values of 'ident', and columns correspond to 'variables'. Each element of the matrix represents the median of a specific variable for a specific group. If 'return_matrix' is FALSE, it saves a heatmap plot and returns the plot object.

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