exprTopHeatmap: Expression Heatmap

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Expression Heatmap

Description

plot a heatmap of expression matrix

Usage

exprTopHeatmap(
  expr,
  group_list,
  filename = NA,
  top = 1000,
  main = "SD Top 1000 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

Can filter genes by 'top'. 'top' means the top sd (by sd) of expression matrix.

Value

a heatmap or a file

Examples

exprTopHeatmap(expr,group_list)

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