zheat_v2: Z-score normalized heatmap of gene expression
In kevincjnixon/BinfTools: Useful functions for standard analyses

zheat_v2

R Documentation

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_v2(
  genes = NULL,
  counts,
  conditions,
  order.by = NULL,
  sort.genes.by = NULL,
  title = "DEGs",
  labgenes = NULL,
  zscore = TRUE,
  avgExp = FALSE,
  rclus = FALSE,
  hmcol = NULL,
  retClus = FALSE,
  annoCols = "Dark2",
  border_color = "grey60",
  cellheight = NA,
  fontsize = 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))
`order.by`	Character vector indicating the arbitrary appearance order of the conditions level. Default is the default order of levels(conditions).
`sort.genes.by`	Character vector indicating the samples for sorting heatmap rows (genes).
`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.
`border_color`	color of cell borders on heatmap, use NA if no border should be drawn.