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Cohen's d Heatmap Function

Source: R/CohenD_IndividualGenes.R
CohenD_IndividualGenes.Rd

This function computes Cohen's d for each gene based on gene expression data and sample metadata. For each gene, it compares the expression values between samples where condition_var equals class (the positive class) versus the remaining samples. The resulting effect sizes are then visualized as a heatmap.

Usage

CohenD_IndividualGenes(
  data,
  metadata,
  genes = NULL,
  condition_var,
  class,
  group_var = NULL,
  title = NULL,
  titlesize = 16,
  params = list()
)

Arguments

data

A data frame or matrix containing gene expression data, with genes as rows and samples as columns.

metadata

A data frame containing sample metadata. The first column should contain sample identifiers that match the column names of data.

genes

A character vector specifying which genes to include. If NULL (default), all genes in data are used. A warning is issued if more than 30 genes are selected.

condition_var

A character string specifying the column name in metadata representing the condition of interest. (Mandatory; no default.)

class

A character string or vector specifying the positive class label for the condition. (Mandatory; no default.)

group_var

An optional character string specifying the column name in metadata used for grouping samples. If not provided (NULL), all samples are treated as a single group.

title

An optional character string specifying a custom title for the heatmap. If not provided, a default title is generated.

titlesize

A numeric value specifying the size of the title. Default is 14.

params

A list of additional parameters for customizing the heatmap. Possible elements include:

cluster_rows

Logical; if TRUE (default), rows are clustered.

cluster_columns

Logical; if TRUE (default), columns are clustered.

colors

A vector of length 2 of colors to be used for the minimum and maximum values of the color scale. Defaults to c("#FFFFFF", "#21975C"), but note that the default mapping for Cohen's d is set to a divergent scale.

limits

A numeric vector of length 2 specifying the minimum and maximum values for the color scale. If not provided, defaults to c(-2, 2).

name

A character string for the legend title of the color scale. Default is "Cohen's d".

row_names_gp

Optional graphical parameters for row names (passed to ComplexHeatmap).

column_names_gp

Optional graphical parameters for column names (passed to ComplexHeatmap).

Value

Invisibly returns a list containing:

plot

The ComplexHeatmap object of the Cohen's d heatmap.

data

A data frame with the calculated Cohen's d values for each gene and group.

Details

This function computes Cohen's d for each gene by comparing the expression values between samples with condition_var == class and those that do not. The effect sizes are then visualized as a heatmap using ComplexHeatmap. When group_var is not provided, all samples are treated as a single group.

Examples

if (FALSE) { # \dontrun{
  result <- CohenDHeatmap(data = myData,
                          metadata = myMetadata,
                          genes = c("Gene1", "Gene2", "Gene3"),
                          condition_var = "Genotype",
                          class = "Mutant",
                          group_var = "CellType",
                          title = "Cohen's d Heatmap",
                          params = list(limits = c(-2, 2)))
} # }