plot_heatmap: Plots heatmap with dendrograms

In nicohuttmann/pOmics: Framework for proteomics data analysis

Plots heatmap with dendrograms

Description

Plots heatmap with dendrograms

Usage

plot_heatmap(
  data_,
  labels.variables,
  labels.observations,
  color.high = "darkred",
  color.mid = "white",
  color.low = "darkblue",
  labels_x = T,
  labels_y = F,
  dend_x = T,
  dend_y = T,
  man.pos.x,
  man.pos.y,
  annot_layer_x,
  annot_layer_y,
  legends,
  ratio = 3,
  rel_dend_x = 0.1,
  rel_dend_y = 0.2,
  rel_labels_x = 0.2,
  rel_labels_y = 0.2,
  rel_annot_layer_x = 0.05,
  rel_annot_layer_y = 0.1,
  rel_legends = 0.25,
  rel_legends_space = 0.05,
  axis.text.x.angle = 45,
  annotation.colors = list(),
  heatmap.legend.title = "",
  dataset,
  view = T,
  export = F,
  file = "heatmap.pdf",
  height = 6,
  input = "data_hclust",
  output = "plot_hclust"
)

Arguments

data_	data
labels.variables	variables data name to use as labels
labels.observations	column in data for observation labels
color.high	color for highest value (default = "darkred")
color.mid	color for middle value (default = "white")
color.low	color for lowest value (default = "darkblue")
labels_x	(logical) plot x-axis labels
labels_y	(logical) plot y-axis labels
dend_x	(logical) plot x-axis dendrogram
dend_y	(logical) plot y-axis dendrogram
man.pos.x	option to manually specify order of x-axis labels (disables) dendrogram
man.pos.y	option to manually specify order of x-axis labels (disables) dendrogram
annot_layer_x	(character) data columns to be included as annotation layers on x-axis
annot_layer_y	(character) data columns to be included as annotation layers on y-axis
legends	name of plot elements for which a legend should be included (full names must be used, e.g. c("annot_layer_x_groups", "heatmap"))
ratio	y/x ratio of heat map
rel_dend_x	relative height of x-axis dendrogram
rel_dend_y	relative width of y-axis dendrogram
rel_labels_x	relative height of x-axis labels
rel_labels_y	relative width of y-axis labels
rel_annot_layer_x	relative height/s of x-axis annotation layers (either one number or vector with number for each)
rel_annot_layer_y	relative width/s of y-axis annotation layers (either one number or vector with number for each)
rel_legends	relative width of legends layer to complete heatmap
rel_legends_space	relative space between plot and legends
axis.text.x.angle	angle of x-axis labels
annotation.colors	(optional) named list containing color vector for annotation layers
heatmap.legend.title	title of heatmap legend
dataset	dataset
view	print plot
export	export plot as pdf
file	file name
height	plot height in inch for export
input	input data name
output	output data name

nicohuttmann/pOmics documentation built on Sept. 21, 2022, 9:28 a.m.