Usage
tanglegram(dend1, ...)
"tanglegram"(dend1, dend2 , sort = FALSE, color_lines, 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 = 2, cex_main_left = cex_main, cex_main_right = cex_main, cex_sub = cex_main, highlight_distinct_edges = TRUE, common_subtrees_color_lines = TRUE, common_subtrees_color_branches = FALSE, faster = FALSE, ...)
"tanglegram"(dend1, which = c(1L,2L), main_left, main_right, ...)
"tanglegram"(dend1, ...)
"tanglegram"(dend1, ...)
Arguments
dend1
tree object (dendrogram/dendlist/hclust/phylo), plotted on the left
dend2
tree object (dendrogram/hclust/phylo), plotted on the right
which
an integer vector of length 2, indicating
which of the trees in the dendlist object should be plotted
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).
The colors in the vector are applied on the lines from the bottom up.
lwd
width of the lines connecting the labels. (default is 3.5)
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.
The default is: c(5,3,5) 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, manually changing dLeaf will affect both trees differently.
In such a case, it is recommanded to manually change dLeaf_left
and dLeaf_right.
This can be especially important when changing the lab.cex of the
dendrogram's labels.
Alternatively, one could manually set the xlim parameter for both
trees, which will force the proportion of distances of the
labels from the trees to remain the same.
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 after you are sure
the labels and orders are correctly aligned.
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.
highlight_distinct_edges
logical (default is TRUE). If to highlight distinct edges in each tree (by changing their line types to 2).
(notice that this can be slow on large trees)
common_subtrees_color_lines
logical (default is TRUE). color the connecting line based on the common subtrees of both dends.
This only works if
(notice that this can be slow on large trees)
common_subtrees_color_branches
logical (default is FALSE).
Color the branches of both dends based on the common subtrees.
(notice that this can be slow on large trees)
This is FALSE by default since it will override the colors of the existing tree.
faster
logical (FALSE). If TRUE, it overrides some other parameters to
have them turned off so that the plotting will go a tiny bit faster.