heatmapplot: Make an expression heatmap with hierarchical clustering

In FerrenaAlexander/FerrenaBulkRNAseq: Pipeline for analysis of bulkRNAseq data

Make an expression heatmap with hierarchical clustering

Description

assumes a normalized counts matrix, should work with TPM too. Currently, color depends on addding metadata. Later, will add support for manually defined colors.

Usage

heatmapplot(
  expmatrix,
  genes,
  metadata,
  heatmaptitle,
  legendtitle,
  do.log2,
  do.scale,
  change_gene_label,
  gene_label_equivalency,
  clustering_distance_columns,
  deres,
  pval_thres,
  lfc_thres,
  use_padj,
  ...
)

Arguments

expmatrix	matrix or data.frame with rows = genes and columns = samples
genes	character vector of gene names (rownames) in the expmatrix
metadata	data.frame in DESeq2 "coldata" format. Needs a "Sample" column with sample IDs matching colnames of expmat, a "Condition" column with the associated conditon, and a "Color" column that has the sample colors
heatmaptitle	string, name of heatmap on top
legendtitle	string, what to call the values in the gene expression matrix. Will default to "Zscaled Normalized Counts"
do.log2	T/F, whether to log2(x+1) transform gene expression values (rows) in the matrix
do.scale	T/F, whether to scale (z-transform, (x - mean(x) / sd(x))) the gene expression values (rows) of the matrix
change_gene_label	T/F, whether to change gene labels, defautl F
gene_label_equivalency	data.frame, if change_gene_label is set to T, need to provide a data.frame with two columns, first column with current gene labels (rownames of res) and second column with gene labels you want to plot as labels. Useful for when you have res with IDs but want to show gene symbols.
clustering_distance_columns	distance to use for ComplexHeatmap::Heatmap clustering of rows, default is pearson
...	Additionaly arguments to pass to ComplexHeatmap::Heatmap

FerrenaAlexander/FerrenaBulkRNAseq documentation built on Oct. 16, 2022, 8:18 a.m.