CorrelationHeatmap: Generate correlation heatmaps with optional grouping

This function generates correlation heatmaps using the ComplexHeatmap package. It allows users to compute correlation matrices for a set of genes and visualize them in a heatmap. If a grouping variable is provided (separate.by), multiple heatmaps are created, each corresponding to a different level of the grouping variable.

Usage

CorrelationHeatmap(
  data,
  metadata = NULL,
  genes,
  separate.by = NULL,
  method = c("pearson", "spearman", "kendall"),
  colorlist = list(low = "blue", mid = "white", high = "red"),
  limits_colorscale = NULL,
  widthTitle = 16,
  title = NULL,
  cluster_rows = TRUE,
  cluster_columns = TRUE,
  detailedresults = FALSE,
  legend_position = c("right", "top"),
  titlesize = 20,
  show_row_names = TRUE,
  show_column_names = TRUE
)

Arguments

data: A numeric counts data frame where rows correspond to genes and columns to samples.
metadata: A data frame containing metadata. Required if separate.by is specified.
genes: A character vector of gene names to be included in the correlation analysis.
separate.by: A character string specifying a column in metadata to separate heatmaps by (e.g., "Condition").
method: Correlation method: "pearson" (default), "spearman", or "kendall".
colorlist: A named list specifying the colors for the heatmap (low, mid, high), corresponding to the limits of the colorscale.
limits_colorscale: A numeric vector of length 3 defining the limits for the color scale (default: min, 0, max).
widthTitle: Numeric value controlling the width of the plot title. Default is 16.
title: A string specifying the main title of the heatmap(s).
cluster_rows: Logical; whether to cluster rows (default = TRUE).
cluster_columns: Logical; whether to cluster columns (default = TRUE).
detailedresults: Logical; if TRUE, additional analysis results are stored in the output list (default = FALSE).
legend_position: Character; position of the legend ("right" - default - or "top").
titlesize: Numeric; font size of the heatmap title (default = 20).
show_row_names: A character string specifying whether row names (genes) should be displayed.
show_column_names: A character string specifying whether column names (samples) should be displayed.

Value

A list containing:

data

Correlation matrices for each condition (or a single matrix if separate.by = NULL).

plot

The generated heatmap object(s).

aux

A list containing additional analysis results if detailedresults = TRUE.

If separate.by is specified:

A list where each element corresponds to a different condition. Each sublist contains:

method: The correlation method used.
corrmatrix: The computed correlation matrix for that condition.
metadata: The subset of metadata corresponding to the condition.
heatmap: The ComplexHeatmap object before being drawn.

If separate.by = NULL (single heatmap case):

A list containing:

method: The correlation method.
corrmatrix: The computed correlation matrix.

Examples

if (FALSE) { # \dontrun{
data_matrix <- matrix(rnorm(100), nrow = 10, ncol = 10)
rownames(data_matrix) <- paste0("Gene", 1:10)
colnames(data_matrix) <- paste0("Sample", 1:10)

# Basic usage
result <- CorrelationHeatmap2(data_matrix, genes = rownames(data_matrix))

# Using metadata to separate by condition
metadata <- data.frame(Sample = colnames(data_matrix),
                       Condition = rep(c("A", "B"), each = 5))
result <- CorrelationHeatmap2(data_matrix, metadata, genes =
rownames(data_matrix), separate.by = "Condition")
} # }