zheat: Z-score normalized heatmap of gene expression

In kevincjnixon/BinfTools: Useful functions for standard analyses

Z-score normalized heatmap of gene expression

Description

A function to generate a z-score normalized heatmap of gene expression from a DESeq2 counts object.

Usage

zheat(
  genes = NULL,
  counts,
  conditions,
  con = "WT",
  title = "DEGs",
  labgenes = NULL,
  zscore = TRUE,
  avgExp = FALSE,
  rclus = FALSE,
  hmcol = NULL,
  retClus = FALSE,
  annoCols = "Dark2",
  fs = 10
)

Arguments

genes	A character vector of genes to subset from rownames(counts) to create the heatmap
counts	Normalized count matrix with rows as genes and columns as samples. Use 'counts(dds, normalized=TRUE)'.
conditions	Character vector indicating conditions belonging to each sample (same order as colnames(counts))
con	Character vector indicating the control condition level in 'conditions'. Default is "WT".
title	Character vector indicating the title of the figure
labgenes	Character vector corresponding to rownames(counts) of genes to be labelled on the side of the heatmap. Leave as NULL to label all genes. Use "" to label no genes.
zscore	Boolean indicating if counts should be z-score normalized (default=TRUE)
avgExp	Boolean indicating if values should be averaged within each condition (i.e. plot one value per condition). Default=FALSE.
rclus	Boolean indicating if rows (genes) should be clustered. Leave FALSE for genes to be ordered on decreasing expression in 'con'.
hmcol	Color ramp palette of length 100 for custom heatmap colouring. Leave NULL for defaults.
retClus	Boolean indicating if clustered row names should be returnd. Default=FALSE.
annoCols	Character vector indicating RColorBrewer palette name or colours for annotation colours if rclus is provided a data.frame.
fs	Numeric indicating font size for row names. Default is 10.

Value

Heatmap of z-score normalized gene expression with control condition samples appearing first.

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.