dendextend (version 0.16.1)

set: Set (/update) features to a dendrogram

Description

a master function for updating various attributes and features of dendrogram objects.

Usage

set(object, ...)

## S3 method for class 'dendrogram':
set(object,
   what = c("labels",
            "labels_colors",
            "labels_cex",
            "leaves_pch",
            "leaves_cex",
            "leaves_col",
            "hang_leaves",
            "branches_k_color",
            "branches_col",
            "branches_lwd",
            "branches_lty",
            "by_labels_branches_col",
            "by_labels_branches_lwd",
            "by_labels_branches_lty",
            "clear_branches",
            "clear_leaves"
   ),
   value, ...)

## S3 method for class 'dendlist':
set(object, ..., which)

Arguments

object

a tree (dendrogram, or dendlist)

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 tree. (the type of the value depends on the "what")

...

passed to the specific function for more options.

which

an integer vector indicating, in the case "object" is a dendlist, on which of the trees should the modification be performed. If missing - the change will be performed on all of objects in the dendlist.

Value

• An updated dendrogram (or dendlist), with some change to the parameters of it

Details

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. You can read more about them here: branches_attr_by_labels

See Also

labels<-.dendrogram, labels_colors<-, hang.dendrogram, color_branches, assign_values_to_leaves_nodePar, assign_values_to_branches_edgePar, remove_branches_edgePar, remove_leaves_nodePar, noded_with_condition, branches_attr_by_labels, dendrogram

Examples

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_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

#----------------------------
# 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





#----------------------------
# 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
##
require(magrittr)
Rowv_dend <- x %>% dist %>% hclust %>%
   as.dendrogram %>%
   set("branches_k", k = 3) %>%
   set("branches_lwd", 2) %>%  rotate_DendSer
Colv_dend <- t(x) %>% dist %>% hclust %>%
   as.dendrogram %>%
   set("branches_k", k = 3) %>%
   set("branches_lwd", 2) %>%  rotate_DendSer
heatmap.2(x, Rowv = Rowv_dend, Colv = Colv_dend)