dendextend (version 0.14.2)

tanglegram: Tanglegram plot

Description

Counts the number of leaves in a tree (dendrogram or hclust).

Usage

tanglegram(tree1, ...)

## S3 method for class 'dendrogram':
tanglegram(tree1, tree2 ,
   sort = FALSE,
   color_lines = "darkgrey",
   lwd = 3.5,
   edge.lwd = NULL,
   columns_width = c(5,3,5),
   margin_top = 3,
   margin_bottom = 2.5,
   margin_inner = 3,
   margin_outer = 0.5,
   left_dendo_mar = c(margin_bottom,margin_outer,margin_top,margin_inner),
   right_dendo_mar = c(margin_bottom,margin_inner,margin_top,margin_outer),
   intersecting = TRUE,
   dLeaf = NULL,
   dLeaf_left = dLeaf,
   dLeaf_right = dLeaf,
   axes = TRUE,
   type = "r", # can also be "t"
   lab.cex = NULL,
   remove_nodePar =FALSE,
   main = "",
   main_left = "",
   main_right = "",
   sub = "",
   k_labels = NULL,
   k_branches = NULL,
   rank_branches = FALSE,
   hang = FALSE,
   match_order_by_labels = TRUE,
   cex_main = 3,
   cex_main_left = cex_main,
   cex_main_right = cex_main,
   cex_sub = cex_main,
   ...)

## S3 method for class 'hclust':
tanglegram(tree1, ...)

## S3 method for class 'phylo':
tanglegram(tree1, ...)

Arguments

tree1

tree object (dendrogram/hclust/phylo), plotted on the left

tree2

tree object (dendrogram/hclust/phylo), plotted on the right

sort

logical (FALSE). Should the dendrogram's labels be "sorted"? (might give a better tree in some cases).

color_lines

a vector of colors for the lines connected the labels. If the colors are shorter than the number of labels, they are recycled (and a warning is issued).

lwd

width of the lines connecting the labels.

edge.lwd

width of the dendrograms lines.

columns_width

a vector with three elements, giving the relative sizes of the the three plots (left dendrogram, connecting lines, right dendrogram). This is passed to layout.

margin_top

the number of lines of margin to be specified on the top of the plots.

margin_bottom

the number of lines of margin to be specified on the bottom of the plots.

margin_inner

margin_bottom the number of lines of margin to be specified on the inner distence between the dendrograms and the connecting lines.

margin_outer

margin_bottom the number of lines of margin to be specified on the outer distence between the dendrograms and the connecting lines.

left_dendo_mar

mar parameters of the left dendrgoram.

right_dendo_mar

mar parameters of the right dendrgoram.

intersecting

logical (TRUE). Should the leaves of the two dendrograms be pruned so that the two trees will have the same labels?

dLeaf

a number specifying the distance in user coordinates between the tip of a leaf and its label. If NULL, as per default, 3/4 of a letter width or height is used. Notice that if we are comparing two dendrograms with different heights, manual

dLeaf_left

dLeaf of the left dendrogram, by default it is equal to dLeaf (often negative).

dLeaf_right

dLeaf of the right dendrogram, by default it is equal to minus dLeaf (often positive).

axes

logical (TRUE). Should plot axes be plotted?

type

type of plot ("t"/"r" = triangle or rectangle)

lab.cex

numeric scalar, influanicing the cex size of the labels.

remove_nodePar

logical (FALSE). Should the nodePar of the leaves be removed? (useful when the trees' leaves has too many parameters on them)

main

Character. Title above the connecting lines.

main_left

Character. Title of the left dendrogram.

main_right

Character. Title of the right dendrogram.

sub

Character. Title below the connecting lines.

k_labels

integer. Number of groups by which to color the leaves.

k_branches

integer. Number of groups by which to color the branches.

rank_branches

logical (FALSE). Should the branches heights be adjusted? (setting this to TRUE - can make it easier for comparing topological differences)

hang

logical (FALSE). Should we hang the leaves of the trees?

match_order_by_labels

logical (TRUE). Should the leaves value order be matched between the two trees based on labels? This is a MUST in order to have the lines connect the correct labels. Set this to FALSE if you want to make the plotting a bit faster, and only aft

cex_main

A numerical value giving the amount by which plotting title should be magnified relative to the default.

cex_main_left

see cex_main.

cex_main_right

see cex_main.

cex_sub

see cex_main.

...

not used.

Value

• An invisible list, with two trees after being modified during the creation of the tanglegram.

source

The function is based on code from plannapus, after major revisions. See: http://stackoverflow.com/questions/12456768/duelling-dendrograms-in-r-placing-dendrograms-back-to-back-in-r

Details

Notice that tanglegram does not "resize" well. In case you are resizing your window you would need to re-run the function.

See Also

remove_leaves_nodePar, plot_horiz.dendrogram, rank_branches, hang.dendrogram

Examples

set.seed(23235)
ss <- sample(1:150, 10 )
hc1 <- hclust(dist(iris[ss,-5]), "com")
hc2 <- hclust(dist(iris[ss,-5]), "single")
dend1 <- as.dendrogram(hc1)
dend2 <- as.dendrogram(hc2)
tanglegram(dend1 , dend2)
tanglegram(dend1 , dend2, sort = TRUE)
tanglegram(dend1 , dend2, remove_nodePar = TRUE)
tanglegram(dend1 , dend2, k_labels = 6, k_branches = 4)

tanglegram(dend1 , dend2, lab.cex = 2, edge.lwd = 3,
margin_inner= 5, type = "t", center = TRUE)


## works nicely:
tanglegram(dend1 , dend2, lab.cex = 2, edge.lwd = 3,
margin_inner= 3.5, type = "t", center = TRUE,
dLeaf = -0.1, xlim = c(7,0),
k_branches=3)


# using rank_branches can make the comparison even easier
tanglegram(rank_branches(dend1) , rank_branches(dend2), lab.cex = 2, edge.lwd = 3,
 margin_inner= 3.5, type = "t", center = TRUE,
  dLeaf = -0.1, xlim = c(5.1,0), columns_width= c(5,1,5),
   k_branches=3)