zheatmap: Clustered Heatmap

In zhuchcn/zheatmap: Heatmap With Dendrograms

Description

A flexible heatmap function with dendrograms on both sides.

Usage

zheatmap(data, colSideBar = NULL, rowSideBar = NULL, Rowv = TRUE,
  Colv = TRUE, colors = viridis(n = 256, alpha = 1, begin = 0, end = 1,
  option = "viridis"), line.color = "white", line.size = 0,
  seriate = "OLO", scale = c("column", "row", "none"),
  scale.fun = c("scale", "absolute_scale"), xtext = FALSE,
  ytext = TRUE, text.size = 12, xtext.angle = 0, ytext.angle = 0,
  xtext.hjust = 1, xtext.vjust = 0, ytext.hjust = 1,
  ytext.vjust = 0, legend.text.size = 9, show.legend.scale = FALSE,
  show.value = FALSE, text.data = NULL, text.value.size = text.size,
  text.value.cutoff = c(-Inf, Inf), heights, widths, print = TRUE)

Arguments

data	a data.frame object
colSideBar	a character or factor vector to annotate on the column side between the heatmap ans column-wize dendrogram
Rowv	a logical value whether to show the row-wise dendrogram
Colv	a logical value whether to show the column-wise dendrogram
colors	a character vector off colors to use. The default uses viridis(n=256, alpha = 1, begin = 0, end = 1, option = "viridis")
seriate	character indicates the method to use to calculate the dist. Usful methods include "OLO", "GW", and "HC". See seriate for more detail
scale	A character value indicates whether the data should be scaled column wise or row wise, or not scaled.
scale.fun	the scale function to use. When using "scale" the scale from base package will be used. When using "absolute_scale" each row or column will be forced between -1 and 1.
xtext	logic whether to show x axis labels
ytext	logic whether to show y axis labels
text.size	numeric
xtext.angle	numeric
ytext.angle	numeric
xtext.hjust	numeric
xtext.vjust	numeric
ytext.hjust	numeric
ytext.vjust	numeric
show.legend.scale	logic value whether to show scales on color key. Default is TRUE.
show.value	bolean, whether show values on heatmap
heights	numeric vector with length of 2
print	logic, whether to print the heatmap out or not. Default is TRUE and if FALSE, a grob object will be returned
value.cutoff	numeric, length bust be 2. All values beyond this range
value.size	numeric, the size of values to display will displayed as "< ..." or "> ..."
width	numeric vector with length of 2

Author(s)

Chenghao Zhu

Examples

# using the mtcars data
zheatmap(mtcars)

# show x axis texts and rotate them 90 degree
zheatmap(t(mtcars), scale = "row", xtext.angle = 90)

# change the color
library(RColorBrewer)
my_colors = colorRampPalette(rev(brewer.pal(11, "RdBu")))(256)
zheatmap(mtcars, colors = my_colors)

# use hierachical clustring method
zheatmap(mtcars, seriate = "HC")

# hide the column wise dendrogram
zheatmap(mtcars, Colv = F)

# use color side bar to annotate
zheatmap(mtcars[,-2], rowSideBar = factor(mtcars$cyl))

zhuchcn/zheatmap documentation built on July 18, 2019, 3:14 p.m.