dendextend (version 1.4.0)

pvclust_show_signif: 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)