Plot a Proteomics Heatmap — plot_proteomics

Generates a heatmap of protein expression. The function can operate in two modes depending on the condition argument.

Individual Samples (default): If condition is NULL, a heatmap of all individual samples is generated, with samples clustered by similarity.
Summarized Conditions: If a condition is provided, the function first calculates the mean expression for each protein across the replicates within each condition group, then generates a heatmap of these mean values.

In both modes, the data is row-wise Z-scored before plotting.

Usage

plot_proteomics_heatmap(
  object,
  protmeta_col = NULL,
  genes = NULL,
  title = NULL,
  condition = NULL
)

# S4 method for class 'SummarizedExperiment'
plot_proteomics_heatmap(
  object,
  protmeta_col = NULL,
  genes = NULL,
  title = NULL,
  condition = NULL
)

Arguments

object: A SummarizedExperiment object. It is recommended to use data that has been log-transformed and imputed.
protmeta_col: A character string specifying the name of the column in the rowData slot to use for protein labels on the heatmap rows. Defaults to the first column of rowData.
genes: Optional. A character vector of gene or protein names to subset the data to. Only these proteins will be included in the heatmap. The match is case-insensitive.
title: Optional. A character string for the plot title.
condition: Optional. A character string specifying a column name in the colData slot. If provided, triggers the summarized heatmap mode.

Value

A ggplot object representing the heatmap.

Functions

plot_proteomics_heatmap(SummarizedExperiment): Method for SummarizedExperiment objects.