plot_heatmap_discrete: Plots heatmap with dendrograms

In nicohuttmann/pOmics: Framework for proteomics data analysis

Plots heatmap with dendrograms

Description

Plots heatmap with dendrograms

Plots heatmap from discrete values

Usage

plot_heatmap_discrete(
  data,
  transform = T,
  clustering.method = "complete",
  order.y = T,
  order.x = T,
  colors,
  labels,
  legend.title = NULL,
  legend.text.align = 0,
  ratio = 1,
  label.fun
)

plot_heatmap_discrete(
  data,
  transform = T,
  clustering.method = "complete",
  order.y = T,
  order.x = T,
  colors,
  labels,
  legend.title = NULL,
  legend.text.align = 0,
  ratio = 1,
  label.fun
)

Arguments

data	data frame with first column variables
transform	should data be transformed?
clustering.method	argument for hclust
order.y	either T/F if axis should be reordered by dendrogram, or vector containing all axis labels in order
order.x	either T/F if axis should be reordered by dendrogram, or vector containing all axis labels in order
colors	named vector of colors with names as corresponding values
labels	named vector of labels with names as corresponding values
legend.title	title of legend
legend.text.align	0 = left, 1 = right
ratio	x-y-ratio of heatmap tiles
label.fun	function to generate labels with
data_	data
transpose	should data be transformed
protein.label.FUN	function for protein labels
observation.labels	column for observation labels
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
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
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)
axis.text.x.angle	angle of x-axis labels
annotation.colors	(optional) named list containing color vector for annotation layers
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"))
rel_legends	relative width of legends layer to complete heatmap
rel_legends_space	relative space between plot and legends
heatmap.legend.title	title of heatmap legend
dataset	dataset
file	file name
view	print plot
export	export plot as pdf
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.