heatmap_calc_clust_median: Calculate and plot heatmap of cluster medians

View source: R/Seurat.Utils.Metadata.R

heatmap_calc_clust_medianR Documentation

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.