Ladderize a Tree
This function reorganizes the internal structure of the tree to get the ladderized effect when plotted.
ladderize(x, right = TRUE, ...) ## S3 method for class 'dendrogram' ladderize(x, right = TRUE, ...) ## S3 method for class 'phylo' ladderize(x, right = TRUE, phy, ...) ## S3 method for class 'dendlist' ladderize(x, right = TRUE, which, ...)
x |
a tree object (either a dendrogram, dendlist, or phylo) |
right |
a logical (TRUE) specifying whether the smallest clade is on the right-hand side (when the tree is plotted upwards), or the opposite (if FALSE). |
... |
Currently ignored. |
phy |
a placeholder in case the user uses "phy =" |
which |
an integer (can have any number of elements). It indicates the elements in the dendlist to ladderize. If missing, it will ladderize all the dendrograms in the dendlist. |
A rotated tree object
ladderize,
rev.dendrogram, rotate (dendextend), rotate (ape)
dend <- USArrests[1:8, ] %>%
dist() %>%
hclust() %>%
as.dendrogram() %>%
set("labels_colors") %>%
set("branches_k_color", k = 5)
set.seed(123)
dend <- shuffle(dend)
par(mfrow = c(1, 3))
dend %>% plot(main = "Original")
dend %>%
ladderize(TRUE) %>%
plot(main = "Right (default)")
dend %>%
ladderize(FALSE) %>%
plot(main = "Left (rev of right)")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.