Set (/update) features to a dendrogram
a master function for updating various attributes and features of dendrogram objects.
set(dend, ...)
## S3 method for class 'dendrogram'
set(
dend,
what = c("labels", "labels_colors", "labels_cex", "labels_to_character",
"leaves_pch", "leaves_cex", "leaves_col", "nodes_pch", "nodes_cex", "nodes_col",
"hang_leaves", "rank_branches", "branches_k_color", "branches_k_lty", "branches_col",
"branches_lwd", "branches_lty", "by_labels_branches_col", "by_labels_branches_lwd",
"by_labels_branches_lty", "by_lists_branches_col", "by_lists_branches_lwd",
"by_lists_branches_lty", "highlight_branches_col", "highlight_branches_lwd",
"clear_branches", "clear_leaves"),
value,
order_value = FALSE,
...
)
## S3 method for class 'dendlist'
set(dend, ..., which)
## S3 method for class 'data.table'
set(...)dend |
a tree (dendrogram, or dendlist) |
... |
passed to the specific function for more options. |
what |
a character indicating what is the property of the tree that should be set/updated. (see the usage and the example section for the different options) |
value |
an object with the value to set in the dendrogram tree. (the type of the value depends on the "what") |
order_value |
logical. Default is FALSE. If TRUE, it means the order of the value is in the order of the data which produced the hclust or dendrogram - and will reorder the value to conform with the order of the labels in the dendrogram. |
which |
an integer vector indicating, in the case "dend" is a dendlist, on which of the trees should the modification be performed. If missing - the change will be performed on all of dends in the dendlist. |
This is a wrapper function for many of the main tasks we might wish to perform on a dendrogram before plotting.
The options of by_labels_branches_col, by_labels_branches_lwd, by_labels_branches_lty have extra parameters: type, attr, TF_value, and by_lists_branches_col, by_lists_branches_lwd, by_lists_branches_lty have extra parameters: attr, TF_value. You can read more about them here: branches_attr_by_labels and branches_attr_by_lists
The "what" parameter" can accept the following options:
labels - set the labels (labels<-.dendrogram)
labels_colors - set the labels' colors (color_labels)
labels_cex - set the labels' size (assign_values_to_leaves_nodePar)
labels_to_character - set the labels' to be characters
leaves_pch - set the leaves' point type (assign_values_to_leaves_nodePar). A leave is the terminal node of the tree.
leaves_cex - set the leaves' point size (assign_values_to_leaves_nodePar). For using this you MUST also set leaves_pch, a good value to use is 19.
leaves_col - set the leaves' point color (assign_values_to_leaves_nodePar). For using this you MUST also set leaves_pch, a good value to use is 19.
nodes_pch - set the nodes' point type (assign_values_to_nodes_nodePar)
nodes_cex - set the nodes' point size (assign_values_to_nodes_nodePar)
nodes_col - set the nodes' point color (assign_values_to_nodes_nodePar)
hang_leaves - hang the leaves (hang.dendrogram)
branches_k_color - color the branches (color_branches), a k parameter needs to be supplied.
branches_k_lty - updates the lwd of the branches (similar to branches_k_color), a k parameter needs to be supplied.
branches_col - set the color of branches (assign_values_to_branches_edgePar)
branches_lwd - set the line width of branches (assign_values_to_branches_edgePar)
branches_lty - set the line type of branches (assign_values_to_branches_edgePar)
by_labels_branches_col - set the color of branches with specific labels (branches_attr_by_labels)
by_labels_branches_lwd - set the line width of branches with specific labels (branches_attr_by_labels)
by_labels_branches_lty - set the line type of branches with specific labels (branches_attr_by_labels)
by_lists_branches_col - set the color of branches from the root of the tree down to (possibly inner) nodes with specified members (branches_attr_by_lists)
by_lists_branches_lwd - set the line width of branches from the root of the tree down to (possibly inner) nodes with specified members (branches_attr_by_lists)
by_lists_branches_lty - set the line type of branches from the root of the tree down to (possibly inner) nodes with specified members (branches_attr_by_lists)
highlight_branches_col - highlight branches color based on branches' heights (highlight_branches_col)
highlight_branches_lwd - highlight branches line-width based on branches' heights (highlight_branches_lwd)
clear_branches - clear branches' attributes (remove_branches_edgePar)
clear_leaves - clear leaves' attributes (remove_branches_edgePar)
An updated dendrogram (or dendlist), with some change to the parameters of it
## Not run:
set.seed(23235)
ss <- sample(1:150, 10)
# Getting the dend object
dend <- iris[ss, -5] %>%
dist() %>%
hclust() %>%
as.dendrogram()
dend %>% plot()
dend %>% labels()
dend %>%
set("labels", 1:10) %>%
labels()
dend %>%
set("labels", 1:10) %>%
plot()
dend %>%
set("labels_color") %>%
plot()
dend %>%
set("labels_col", c(1, 2)) %>%
plot() # Works also with partial matching :)
dend %>%
set("labels_cex", c(1, 1.2)) %>%
plot()
dend %>%
set("leaves_pch", NA) %>%
plot()
dend %>%
set("leaves_pch", c(1:5)) %>%
plot()
dend %>%
set("leaves_pch", c(19, 19, NA)) %>%
set("leaves_cex", c(1, 2)) %>%
plot()
dend %>%
set("leaves_pch", c(19, 19, NA)) %>%
set("leaves_cex", c(1, 2)) %>%
set("leaves_col", c(1, 1, 2, 2)) %>%
plot()
dend %>%
set("hang") %>%
plot()
dend %>%
set("branches_k_col") %>%
plot()
dend %>%
set("branches_k_col", c(1, 2)) %>%
plot()
dend %>%
set("branches_k_col", c(1, 2, 3), k = 3) %>%
plot()
dend %>%
set("branches_k_col", k = 3) %>%
plot()
dend %>%
set("branches_k_lty", k = 3) %>%
plot()
dend %>%
set("branches_k_col", k = 3) %>%
set("branches_k_lty", k = 3) %>%
plot()
dend %>%
set("branches_col", c(1, 2, 1, 2, NA)) %>%
plot()
dend %>%
set("branches_lwd", c(2, 1, 2)) %>%
plot()
dend %>%
set("branches_lty", c(1, 2, 1)) %>%
plot()
# clears all of the things added to the leaves
dend %>%
set("labels_color", c(19, 19, NA)) %>%
set("leaves_pch", c(19, 19, NA)) %>% # plot
set("clear_leaves") %>% # remove all of what was done until this point
plot()
# Different order
dend %>%
set("leaves_pch", c(19, 19, NA)) %>%
set("labels_color", c(19, 19, NA)) %>%
set("clear_leaves") %>%
plot()
# doing this without chaining (%>%) will NOT be fun:
dend %>%
set("labels", 1:10) %>%
set("labels_color") %>%
set("branches_col", c(1, 2, 1, 2, NA)) %>%
set("branches_lwd", c(2, 1, 2)) %>%
set("branches_lty", c(1, 2, 1)) %>%
set("hang") %>%
plot()
par(mfrow = c(1, 3))
dend %>%
set("highlight_branches_col") %>%
plot()
dend %>%
set("highlight_branches_lwd") %>%
plot()
dend %>%
set("highlight_branches_col") %>%
set("highlight_branches_lwd") %>%
plot()
par(mfrow = c(1, 1))
#----------------------------
# Examples for: by_labels_branches_col, by_labels_branches_lwd, by_labels_branches_lty
old_labels <- labels(dend)
dend %>%
set("labels", seq_len(nleaves(dend))) %>%
set("by_labels_branches_col", c(1:4, 7)) %>%
set("by_labels_branches_lwd", c(1:4, 7)) %>%
set("by_labels_branches_lty", c(1:4, 7)) %>%
set("labels", old_labels) %>%
plot()
dend %>%
set("labels", seq_len(nleaves(dend))) %>%
set("by_labels_branches_col", c(1:4, 7), type = "any", TF_values = c(4, 2)) %>%
set("by_labels_branches_lwd", c(1:4, 7), type = "all", TF_values = c(4, 1)) %>%
set("by_labels_branches_lty", c(1:4, 7), TF_values = c(4, 1)) %>%
plot()
#---- using order_value
# This is probably not what you want, since cutree
# returns clusters in the order of the original data:
dend %>%
set("labels_colors", cutree(dend, k = 3)) %>%
plot()
# The way to fix it, is to use order_value = TRUE
# so that value is assumed to be in the order of the data:
dend %>%
set("labels_colors", cutree(dend, k = 3), order_value = TRUE) %>%
plot()
#----------------------------
# Example for: by_lists_branches_col, by_lists_branches_lwd, by_lists_branches_lty
L <- list(c("109", "123", "126", "145"), "29", c("59", "67", "97"))
dend %>%
set("by_lists_branches_col", L, TF_value = "blue") %>%
set("by_lists_branches_lwd", L, TF_value = 4) %>%
set("by_lists_branches_lty", L, TF_value = 3) %>%
plot()
#----------------------------
# A few dendlist examples:
dendlist(dend, dend) %>%
set("hang") %>%
plot()
dendlist(dend, dend) %>%
set("branches_k_col", k = 3) %>%
plot()
dendlist(dend, dend) %>%
set("labels_col", c(1, 2)) %>%
plot()
dendlist(dend, dend) %>%
set("hang") %>%
set("labels_col", c(1, 2), which = 1) %>%
set("branches_k_col", k = 3, which = 2) %>%
set("labels_cex", 1.2) %>%
plot()
#----------------------------
# example of modifying the dendrogram in a heatmap:
library(gplots)
data(mtcars)
x <- as.matrix(mtcars)
rc <- rainbow(nrow(x), start = 0, end = .3)
cc <- rainbow(ncol(x), start = 0, end = .3)
##
##' demonstrate the effect of row and column dendrogram options
##
Rowv_dend <- x %>%
dist() %>%
hclust() %>%
as.dendrogram() %>%
set("branches_k", k = 3) %>%
set("branches_lwd", 2) %>%
ladderize() # rotate_DendSer
Colv_dend <- t(x) %>%
dist() %>%
hclust() %>%
as.dendrogram() %>%
set("branches_k", k = 3) %>%
set("branches_lwd", 2) %>%
ladderize() # rotate_DendSer
heatmap.2(x, Rowv = Rowv_dend, Colv = Colv_dend)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.