The significant branches in a dendrogram, based on a pvclust object
Shows the significant branches in a dendrogram, based on a pvclust object
pvclust_show_signif(
dend,
pvclust_obj,
signif_type = c("bp", "au"),
alpha = 0.05,
signif_value = c(5, 1),
show_type = c("lwd", "col"),
...
)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 |
A dendrogram with updated branches
## 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)
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