plot_heatmap_DEseq: Plot a heatmap of differentially expressed genes for a single...
In eisascience/scCustFx: single-cell custom fxs Package

plot_heatmap_DEseq

R Documentation

Plot a heatmap of differentially expressed genes for a single contrast

Description

This function selects DEGs from a contrast result, optionally applies voom transformation and batch correction, then displays a z‑scored heatmap of expression across samples.

Usage

plot_heatmap_DEseq(
  contrast_df,
  count_mat,
  meta_df,
  cleanBatch = TRUE,
  VoomTrans = FALSE,
  BatchFeat = NULL,
  gene_meta,
  filter = FALSE,
  padj_thr = 0.05,
  absLog2FC_thr = 0.58
)

Arguments

`contrast_df`	A data.frame of DE results with columns: ensembl_ID gene IDs matching rownames of `count_mat` log2FoldChange numeric log2 fold changes padj numeric adjusted p‑values contrast_name character string used for the plot title
`count_mat`	Numeric matrix of raw counts (rows=genes, cols=samples). Row names must match `contrast_df$ensembl_ID`, column names match rownames of `meta_df`.
`meta_df`	Data.frame of sample metadata; rows must align with cols of `count_mat`. Must include the column named by `BatchFeat` for batch removal and optionally `PD1status`, `seqrun` for annotations.
`cleanBatch`	Logical; if `TRUE`, calls `limma::removeBatchEffect` on `BatchFeat`. Default `TRUE`.
`VoomTrans`	Logical; if `TRUE`, applies `limma::voom` before batch correction. Default `FALSE`.
`BatchFeat`	Character; the column name in `meta_df` indicating batch. Required when `cleanBatch = TRUE`.
`gene_meta`	Data.frame mapping `ensembl_ID` (rownames) to final gene names. Must contain column `final_GeneName`.
`filter`	Logical; if `TRUE`, DEGs are filtered by `padj` and `absLog2FC`. Default `FALSE`.
`padj_thr`	Numeric cutoff for adjusted p‑value when `filter=TRUE`. Default `0.05`.
`absLog2FC_thr`	Numeric cutoff for absolute log2 fold‑change when `filter=TRUE`. Default `0.58`.