pl_heatmap: plot heatmap using pheatmap

In zzwch/convgene: This package is designed to conveniently convert gene between human and mouse.

Description

plot heatmap using pheatmap

Usage

pl_heatmap(
  data,
  features = NULL,
  color = gradient_colors$f_BuWtRd(99, interpolate = "linear"),
  meta_data = NA,
  annot_col = NA,
  permutation_by = NA,
  seed = 666,
  feature_data = NA,
  annot_row = NA,
  smooth_n = NA,
  do_scale = F,
  smooth_lowess = F,
  lowess_span = 2/3,
  cap_max = NA,
  cap_min = NA,
  annot_colors = NA,
  rownames_to_show = NA,
  ...
)

Arguments

data	feature by cell data matrix
features	features to display
color	heatmap colors
meta_data	cell annotation data frame
annot_col	select colnames of meta_data
permutation_by	permutate and order the cells
seed	permutation seed
feature_data	feature annotation data frame
annot_row	select colnames of feature_data
smooth_n	smooth the expression over smooth_n cells
do_scale	scale data
smooth_lowess	smooth using lowess regression
lowess_span	lowess span
cap_max	capping the maximum of data
cap_min	capping the minimum of data
annot_colors	a list of annotation colors named with annotation categories
rownames_to_show	select rownames to show to the right
...	other params passed to pheatmap

Value

a pheatmap

zzwch/convgene documentation built on July 11, 2021, 9:41 a.m.