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

pvclust_show_signif_gradient {dendextend} | R Documentation

## 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)

[Package dendextend version 1.8.0 Index]