CorrPlotHeatmap: CorrPlotHeatmap

In inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis

CorrPlotHeatmap

Description

Plot a correlation heatmap of top variable genes across samples.

Usage

CorrPlotHeatmap(
  x,
  scale,
  Color,
  type,
  display,
  round_number,
  cutree_rows,
  cutree_cols,
  cluster,
  show_names,
  NumGenes
)

Arguments

x	Numeric matrix of log-CPM values (genes × samples), e.g., from "edgeR::cpm()".
scale	Character. Scaling mode for the heatmap: "row", "column", or "none".
Color	Character. Name of a continuous palette from the "paletteer" package.
type	Character. Correlation method passed to "Hmisc::rcorr()": "pearson", "spearman", or "kendall".
display	Character. Which matrix to display: "correlation" (coefficients) or "pvalue".
round_number	Integer. Number of decimal places to round displayed numbers.
cutree_rows	Integer. Number of clusters to cut for row dendrogram.
cutree_cols	Integer. Number of clusters to cut for column dendrogram.
cluster	Character. Clustering mode: one of "both", "row", "column", or "none".
show_names	Character. One of "both", "row", "column", or "none" to display row/column labels.
NumGenes	Integer. Number of top-variance genes to include in the correlation.

Details

This function selects the highest-variance genes from a log-CPM matrix, computes pairwise correlation coefficients (or p-values) with "Hmisc::rcorr()", and renders a heatmap via "pheatmap", with options for clustering, scaling, and number display.

1. Compute per-gene variance and select the top "NumGenes".

2. Subset the matrix and compute correlations (and p-values) via "Hmisc::rcorr()".

3. Choose to display correlation coefficients or p-values, rounded to "round_number".

4. Determine clustering and label visibility from cluster and "show_names".

5. Render the heatmap with "pheatmap::pheatmap()", passing in custom distance, color, clustering, and "display" number settings, saving to a temporary file to suppress autosave.

Value

A "pheatmap" object representing the correlation heatmap with clustering.

inDAGO documentation built on Aug. 8, 2025, 7:47 p.m.