exprHKGheatmap: Human housekeeping genes Heatmap

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Human housekeeping genes Heatmap

Description

plot a heatmap of highly uniform and strongly expressed Human housekeeping genes

Usage

exprHKGheatmap(
  expr,
  group_list,
  filename = NA,
  main = "Human housekeeping genes",
  hk = c("C1orf43", "CHMP2A", "EMC7", "GPI", "PSMB2", "PSMB4", "RAB7A", "REEP5",
    "SNRPD3", "VCP", "VPS29"),
  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 = 10 * 0.3 + 2.2,
  ...,
  heatmapParam = list(show_rownames = T, cluster_cols = F)
)

Arguments

expr	a expression matrix
group_list	a character vector order by samples
filename	file name you want to save plot
main	plot title
hk	strongly expressed genes
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
top	if not NA, only keep top of genes by mad

Details

Human housekeeping genes revisited in
https://www.tau.ac.il/~elieis/HKG/
E. Eisenberg and E.Y. Levanon, Trends in Genetics, 29 (2013)

Value

a heatmap or a file

Examples

exprHKGheatmap(expr,group_list)

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