| pvclust_show_signif {dendextend} | R Documentation |
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
pvclust_show_signif, pvclust_show_signif_gradient
## 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)