pl_averageHeatmap: Heatmap of average expression of select features

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

Description

Heatmap of average expression of select features

Usage

pl_averageHeatmap(
  data,
  features,
  group_by,
  groups = NULL,
  method = base::mean,
  by_log = F,
  log_base = base::exp(1),
  exclude_zero = F,
  outlier_cutoff = 1,
  heat_color = c("darkblue", "royalblue", "grey100", "tomato", "brown"),
  scale_feature = T,
  cap_max = 2,
  cap_min = -2,
  cluster_rows = F,
  cluster_cols = F,
  show_rownames = F,
  ...
)

Arguments

data	expression matrix of feature by cell, ususally normalized (in log scale) but not feature scaled.
features	features to be visualized
group_by	a vector including cell annotations
groups	only these selected groups to be visualized
method	using base::mean or stats::median or your custom function for each feature vector;
by_log	calculate by log scale ; If TRUE log_base will be ignored.
log_base	base::exp(1) or 2 or other else, depends on your normalization method.
exclude_zero	exclude zeros when calculate average/median feature value. Note exclude_zero first, outlier_cutoff second.
outlier_cutoff	sometimes outliers (several extremely high cells) should be excluded when do summarise. Set 0.99 to exclude top 1 percent cells. (default: 1)
heat_color	heatmap colors
scale_feature	whether do scale by feature
cap_max	if scale_feature, set cap for max
cap_min	if scale_feature, set cap for min
cluster_rows	row clustering
cluster_cols	column clustering
show_rownames	show rownames
...

Value

a pheatmap object

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