plot_heatmap: Plot heatmap using ComplexHeatmap using simplified interface

In keshavmot2/ggexp: Publication Quality Exploratory Data Visualization Using ggplot2

Description

Plot heatmap using ComplexHeatmap using simplified interface

Usage

plot_heatmap(
  matrix,
  row_annotations = NULL,
  column_annotations = NULL,
  one_hot_row_annotations = NULL,
  one_hot_column_annotations = NULL,
  palette = list(),
  split_rows = NULL,
  split_columns = NULL,
  cluster_rows = TRUE,
  cluster_columns = TRUE,
  show_row_dend = TRUE,
  show_column_dend = TRUE,
  show_row_names = TRUE,
  show_column_names = TRUE,
  show_legend_row = colnames(row_annotations),
  show_legend_column = colnames(column_annotations),
  legend_position = "side",
  lower_quantile = 0.01,
  upper_quantile = 0.99,
  text_size = 10,
  row_names_size = 4,
  column_names_size = 4,
  heatmap_color = c("BWR", "cividis", "viridis", "plasma", "magma", "inferno"),
  color_by_quantile = TRUE,
  value_name = "value",
  title = character(0)
)

Arguments

matrix	matrix to plot
row_annotations	data frame with annotations for the rows of the matrix
column_annotations	data frame with annotations for the columns of the matrix
one_hot_row_annotations	data frame with annotations for the rows of the matrix that are to be one-hot encoded
one_hot_column_annotations	data frame with annotations for the columns of the matrix that are to be one-hot encoded
palette	named list of named character vectors with the values being the colors if discrete, or in the form c(colors = XXX, breaks = XXX) if continuous
split_rows	columns of row_annotations to split heatmap rows by
split_columns	columns of column_annottations to split heatmap columns by
cluster_rows	boolean to cluster rows or not
cluster_columns	boolean to cluster columns or not
show_row_dend	boolean to show row dendrogram or not
show_column_dend	boolean to show column dendrogram or not
show_row_names	boolean to show row names or not
show_column_names	boolean to show column names or not
show_legend_row	columns of row_annotations to show legend for
show_legend_column	columns of column_annotations to show legend for
legend_position	either "right" or "bottom"
lower_quantile	lower quantile of data for colorbar
upper_quantile	upper quantile of data for colorbar
text_size	text size
row_names_size	text size for row names
column_names_size	text size for column names
heatmap_color	one of BWR (blue-white-red), cividis, viridis, plasma, magma, or inferno
color_by_quantile	whether to space color values in color bar by quantile or not
value_name	name of value, written above color bar
title	title of plot

keshavmot2/ggexp documentation built on Feb. 6, 2021, 1:38 a.m.