pvclust_show_signif: The significant branches in a dendrogram, based on a pvclust...

In dendextend: Extending 'dendrogram' Functionality in R

The significant branches in a dendrogram, based on a pvclust object

Description

Shows the significant branches in a dendrogram, based on a pvclust object

Usage

pvclust_show_signif(
  dend,
  pvclust_obj,
  signif_type = c("bp", "au"),
  alpha = 0.05,
  signif_value = c(5, 1),
  show_type = c("lwd", "col"),
  ...
)

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.
alpha	a number between 0 to 1, default is .05. Indicates what is the cutoff from which branches will be updated.
signif_value	a 2d vector (deafult: c(5,1)), with the first element tells us what the significant branches will get, and the second element which value the non-significant branches will get.
show_type	a character scalar (either "lwd" or "col"), indicating which parameter of the branches should be updated based on significance.
...	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.