% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/set.dendrogram.R
\name{set}
\alias{set}
\alias{set.dendrogram}
\alias{set.dendlist}
\alias{set.data.table}
\title{Set (/update) features to a dendrogram}
\usage{
set(dend, ...)

\method{set}{dendrogram}(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, ...)

\method{set}{dendlist}(dend, ..., which)

\method{set}{data.table}(...)
}
\arguments{
\item{dend}{a tree (\link{dendrogram}, or \link{dendlist})}

\item{...}{passed to the specific function for more options.}

\item{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)}

\item{value}{an object with the value to set in the dendrogram tree.
(the type of the value depends on the "what")}

\item{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 \link{hclust} 
or \link{dendrogram} - and will reorder the value to conform with the order
of the labels in the dendrogram.}

\item{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.}
}
\value{
An updated dendrogram (or dendlist), with some change to
the parameters of it
}
\description{
a master function for updating various attributes and 
features of dendrogram objects.
}
\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, 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:
\link{branches_attr_by_labels} and \link{branches_attr_by_lists}

The "what" parameter" can accept the following options:

\itemize{
\item{labels - set the labels (\link{labels<-.dendrogram})}
\item{labels_colors - set the labels' colors (\link{color_labels})}
\item{labels_cex - set the labels' size (\link{assign_values_to_leaves_nodePar})}
\item{labels_to_character - set the labels' to be characters}
\item{leaves_pch - set the leaves' point type (\link{assign_values_to_leaves_nodePar}). A leave is the terminal node of the tree.}
\item{leaves_cex - set the leaves' point size (\link{assign_values_to_leaves_nodePar}). For using this you MUST also set leaves_pch, a good value to use is 19.}
\item{leaves_col - set the leaves' point color (\link{assign_values_to_leaves_nodePar}). For using this you MUST also set leaves_pch, a good value to use is 19.}
\item{nodes_pch - set the nodes' point type (\link{assign_values_to_nodes_nodePar})}
\item{nodes_cex - set the nodes' point size (\link{assign_values_to_nodes_nodePar})}
\item{nodes_col - set the nodes' point color (\link{assign_values_to_nodes_nodePar})}
\item{hang_leaves - hang the leaves (\link{hang.dendrogram})}
\item{branches_k_color - color the branches (\link{color_branches}), a \code{k} parameter needs to be supplied.}
\item{branches_k_lty - updates the lwd of the branches (similar to branches_k_color), a \code{k} parameter needs to be supplied.}
\item{branches_col - set the color of branches (\link{assign_values_to_branches_edgePar}) }
\item{branches_lwd - set the line width of branches (\link{assign_values_to_branches_edgePar}) }
\item{branches_lty - set the line type of branches (\link{assign_values_to_branches_edgePar}) }
\item{by_labels_branches_col - set the color of branches with specific labels (\link{branches_attr_by_labels}) }
\item{by_labels_branches_lwd - set the line width of branches with specific labels (\link{branches_attr_by_labels}) }
\item{by_labels_branches_lty - set the line type of branches with specific labels (\link{branches_attr_by_labels}) }
\item{by_lists_branches_col - set the color of branches from the root of the tree down to (possibly inner) nodes with specified members (\link{branches_attr_by_lists}) }
\item{by_lists_branches_lwd - set the line width of branches from the root of the tree down to (possibly inner) nodes with specified members (\link{branches_attr_by_lists}) }
\item{by_lists_branches_lty - set the line type of branches from the root of the tree down to (possibly inner) nodes with specified members (\link{branches_attr_by_lists}) }
\item{highlight_branches_col - highlight branches color based on branches' heights (\link{highlight_branches_col}) }
\item{highlight_branches_lwd - highlight branches line-width based on branches' heights (\link{highlight_branches_lwd}) }
\item{clear_branches - clear branches' attributes (\link{remove_branches_edgePar})}
\item{clear_leaves - clear leaves' attributes (\link{remove_branches_edgePar})}
}
}
\examples{

\dontrun{

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)  





}
}
\seealso{
\link{labels<-.dendrogram}, \link{labels_colors<-},
\link{hang.dendrogram}, \link{color_branches},
\link{assign_values_to_leaves_nodePar},
\link{assign_values_to_branches_edgePar},
\link{remove_branches_edgePar}, \link{remove_leaves_nodePar},
\link{noded_with_condition}, \link{branches_attr_by_labels}, \link{branches_attr_by_lists},
\link{dendrogram}
}
