dendextend (version 1.1.2)

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

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

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)