pl_dotplot: Use dotplot/bubbleplot to visualize average/median and...

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

Description

Use dotplot/bubbleplot to visualize average/median and percentage expression of features (eg. genes) in groups

Usage

pl_dotplot(
  data,
  features,
  group_by,
  groups = NULL,
  method = base::mean,
  by_log = F,
  log_base = base::exp(1),
  exclude_zero = F,
  outlier_cutoff = 1,
  cap_value = NULL,
  swap_axes = F,
  do_scale = F,
  plot_gene_force = F,
  duplicate_features = T,
  gradientn_colors = c("grey90", "grey", "orange", "red", "brown"),
  title = NULL
)

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)
cap_value	the max value to show in dotplot. Any value larger than it will be capped to this value. (default: NA)
swap_axes	swap x-axis and y-axis or not. (default: False)
do_scale	scale the mean value across groups. Useful to demonstrate the differences among groups.
plot_gene_force	Force plot gene, which is missing in data.
duplicate_features	whether display duplicate features or not.
gradientn_colors	the color vector for visualization.
title	title to display in the top.

Value

a ggplot object

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