pvclust_show_signif_gradient: Significance gradient of branches in a dendrogram (via...

In dendextend: Extending 'dendrogram' Functionality in R

Significance gradient of branches in a dendrogram (via pvclust)

Description

Shows the gradient of significance of branches in a dendrogram, based on a pvclust object

Usage

pvclust_show_signif_gradient(
  dend,
  pvclust_obj,
  signif_type = c("bp", "au"),
  signif_col_fun = colorRampPalette(c("black", "darkred", "red")),
  ...
)

Arguments

dend	a dendrogram object
pvclust_obj	a pvclust object
signif_type	a character scalar (either "bp" or "au"), indicating which of the two should be used to update the dendrogram.
signif_col_fun	a function to create colors for the significant gradient. Default is: colorRampPalette(c("black", "darkred", "red"))
...	not used

Value

A dendrogram with updated branches

See Also

pvclust_show_signif, pvclust_show_signif_gradient

Examples

## Not run: 
library(pvclust)
data(lung) # 916 genes for 73 subjects
set.seed(13134)
result <- pvclust(lung[, 1:20], method.dist = "cor", method.hclust = "average", nboot = 100)

dend <- as.dendrogram(result)
result %>%
  as.dendrogram() %>%
  hang.dendrogram() %>%
  plot(main = "Cluster dendrogram with AU/BP values (%)")
result %>% text()
result %>% pvrect(alpha = 0.95)

dend %>%
  pvclust_show_signif(result) %>%
  plot()
dend %>%
  pvclust_show_signif(result, show_type = "lwd") %>%
  plot()
result %>% text()
result %>% pvrect(alpha = 0.95)

dend %>%
  pvclust_show_signif_gradient(result) %>%
  plot()

dend %>%
  pvclust_show_signif_gradient(result) %>%
  pvclust_show_signif(result) %>%
  plot(main = "Cluster dendrogram with AU/BP values (%)\n bp values are highlighted by signif")
result %>% text()
result %>% pvrect(alpha = 0.95)

## End(Not run)

dendextend documentation built on Oct. 13, 2024, 1:06 a.m.