Set (/update) features to a dendrogram

Description

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

Usage

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",
            "clear_branches",
            "clear_leaves"
   ),
   value, ...)
   
## S3 method for class 'dendlist'
set(dend, ..., which)

## S3 method for class 'data.table'
set(...)

Arguments

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

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)

• leaves_cex - set the leaves' point size (assign_values_to_leaves_nodePar)

• leaves_col - set the leaves' point color (assign_values_to_leaves_nodePar)

• 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)

• clear_branches - clear branches' attributes (remove_branches_edgePar)

• clear_leaves - clear leaves' attributes (remove_branches_edgePar)

Value

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

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

## 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 

#----------------------------
# 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
##
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)

Results