exprCorHeatmap: Correlation Heatmap between samples

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Correlation Heatmap between samples

Description

plot a heatmap of correlation between samples

Usage

exprCorHeatmap(
  expr,
  group_list,
  filename = NA,
  top = NA,
  main = "Correlation by all genes",
  palette = RColorBrewer::brewer.pal(3, "Set2")[1:2],
  anno_title = "Group",
  annotation_col = ac_(expr, group_list),
  width = ncol(expr) * 0.3 + 2.2,
  height = ncol(expr) * 0.3 + 2.2,
  ...,
  heatmapParam = list(show_rownames = F)
)

Arguments

expr	a expression matrix
group_list	a character vector order by samples
filename	file name you want to save plot
top	if not NA, only keep top of genes by mad
main	plot title
palette	annotation palette
anno_title	annotation title
annotation_col	annotation dataframe
width	width of plot
height	height of plot
...	more parameters in pheatmap
heatmapParam	more parameters in pheatmap

Details

Use cor to get correlation of samples. Can filter genes by 'top'. 'top' means the top mad (by mad) of expression matrix.

Value

a heatmap plot or a file

Examples

exprCorHeatmap(expr,group_list)

xiayh17/RNAseqStat2 documentation built on May 27, 2023, 12:13 p.m.