pkgdown::build_site() (see:
https://github.com/r-lib/pkgdown/issues/2155). Props to @dmurdoch.dendextendRcpp in some tests and
documentation files (.Rd).k in the output, which is a copy
of nc. This is to make it easier to extract the value
(i.e.: the suggested number of clusters).order_value to easily use
values which are in the order of the original data.just_one paramter.dend %>% set("clear_branches").distinst/tests/ to tests/testthat/colored_barscolor_branches - gained a new “cluster” parameter to allow for easy uneven coloring of branches (using branches_attr_by_clusters). This is not a new feature, as it is an attempt to have the user access more options from one place (i.e.: color_branches).
tanglegram - turned “highlight_distinct_edges = FALSE”. This is due to a bug in R that causes plot.dendrogram to crash when trying to plot a tree with both lty and some character color for the branch.
tanglegram -
plot.ggdend - added support to plot nodes
branches_attr_by_clusters -
dendlist - removed warning when creating an empty dendlist (since we also don’t get a warning when creating a list() )
ladderize - added the which parameter (for
indicating which elements in the dendlist to ladderize)
untangle.dendlist -
dendlist - added the which parameter (for indicating
which elements in the dendlist to pick out)
set
untangle_random_search/untangle_step_rotate_2side/untangle_best_k_to_rotate_by_2side_backNforth - no longer returns a dendlist with names (it shouldn’t, they didn’t have a name to begin with.)
cor.dendlist - added methods “common_nodes”, “FM_index”.
cor_cophenetic - changed method to method_coef (so it could be updated when using cor.dendlist)
use “dend” as a standard name for all the parameters that accept dendrograms (whenever possible, in some cases I preferred to keep another name due to other conventions.)
collapse_branchsort.dendrogram - added a new parameter: type =
c(“labels”, “nodes”), to use ladderize for sortingggplot.ggdend - support theme = NULLas.dendrogram.phylo and
as.phylo.dendrogram functions to it.labels and
labels<-which_node - finds Which node is common to a group of
labelsdendrogram_data (internal) function - a copy of the
function from the ggdendro package (the basis for the new ggdend
class).get_leaves_nodePar - Get nodePar of dendrogram’s leaves
(designed to help with as.ggdend)as.ggdend.dendrogram - turns a dendrogram to the ggdend
class, ready to be plotted with ggplot2.prepare.ggdend - fills a ggdend object with various
default values (to be later used when plotted)ggplot.ggdend - plots a ggdend with the ggplot2 engine
(also the function theme_dendro was imported from the
ggdendro package).remove_nodes_nodePar - as the name implies…collapse_branch - simplifies a tree with branches lower
than some tollerance levelladderize - Ladderize a Tree (reorganizes the internal
structure of the tree to get the ladderized effect when plotted)nleaves.phylo - no longer require conversion to a
dendrogram in order to compute.labels<-.dendrogram - no longer forces as.character
conversiontanglegram - a new highlight_distinct_edges parameter
(default is TRUE)cutree - now produces warnings if it returns 0’s. i.e.:
when it can’t cut the tree based on the required parameter. (following
isue #5 reported by grafab)cutree_1h.dendrogram and
cutree_1k.dendrogram - will now create clusters as the
number of items if k==nleaves(tree) or if h<0. This is both
consistent with stats::hclust, but it also “makes sense” (since this is
well defined for ANY tree). Also updated the tests.get_branches_attr to be
get_root_branches_attrget_nodes_attr - added the “id” parameter (to get
attributes of only a subset of id’s)as.dendrogram.phylo is properly exported now.order.dendrogram<- - commenting off an examples and
tests which (as of R 3.1.1-patched) produces an error (as it should).
Thanks to Prof Brian Ripley for the e-mail about it.cor_bakers_gamma.Rd: lines wider than 90
characterscompacted ‘dendextend-tutorial.pdf’ from 725Kb to 551Kb (doc fixes to pass CRAN checks) (Thanks to using the following:
tools::compactPDF("inst\\doc\\dendextend-tutorial.pdf",
qpdf = "C:\\Program Files (x86)\\qpdf-5.1.2\\bin\\qpdf.exe",
gs_cmd = "C:\\Program Files\\gs\\gs9.14\\bin\\gswin64c.exe",
gs_quality="ebook") And to the help of Prof Brian Ripley and Kurt Hornik )
get_nodes_xy - Get the x-y coordiantes of a
dendrogram’s nodesall_unique - check if all elements in a vector are
uniquehead.dendlistrainbow_fun - uses rainbow_hcl, or rainbow (if
colorspace is not available)warn paramteres are now set to
dendextend_options(“warn”) (which is FALSE)!get_branches_attr - change “warning” to “warn”, and it
now works with is.dendrogram, and no longer changes the class of
something which is not a dendrogram.untangle_step_rotate_2side - print_times is now
dendextend_options(“warn”),color_branches - now handles flat trees more
gracefully. (returns them as they are)cutree.dendrogram - now replaces NA values with 0L (fix
tests for it), added a parameter (NA_to_0L) to control it.Bk - Have it work with cutree(NA_to_0L = FALSE)set.dendrogram - added explenation in the .Rd docs of
the different possible options for “what”set.dendrogram - added nodes_pch, nodes_cex and
nodes_col - using assign_values_to_nodes_nodeParset.dendrogram - changed from using
labels_colors<- to color_labels for
“labels_colors” (this will now work with using k…)set.dendrogram - if “what” is missing, return the
object as is.set.dendrogram - added a “labels_to_char” option.labels_colors<- - added
if(dendextend_options(“warn”))labels<-.dendrogram - if value is missing, returning
the dendrogram as is (this also affects set)get_nodes_attr - can now return an array or a list for
attributes which include a more complex structure (such as nodePar), by
working with lists and adding a “simplify” parameter.rect.dendrogram - a new xpd and lower_rect parameters -
to control how low the rect will be (for example, below or above the
labels). The default is below the labels.colored_bars - added defaults to make the bars be
plotted bellow the labels. +allow the order of the bars to be based on
the labels’ order, made that to be the default +have scale default be
better for multiple bars.branches_attr_by_labels now uses
dendextend_options("warn") to decide if to print that
labels were coerced into character.intersect_trees - now returns a dendlist.untangle - has a default to method (DendSet)untangle_step_rotate_1side - added
“leaves_matching_method” parameter.entanglement.dendrogram - changed the default of
“leaves_matching_method” to be “labels” (slower, but safer for the
user…)branches_attr_by_clusters and
branches_attr_by_labels - moved from using NA to Inf.color_branches - can now work when the labels of the
tree are not unique (“feature”” request by Heather Turner - thanks
Heather :) )rect.dendrogram - fix a bug with the location of the
rect’s (using “tree” and not “dend”)rect.dendrogram - Made sure the heights are working
properly!colored_bars - fix for multiple bars to work.assign_values_to_branches_edgePar,
assign_values_to_nodes_nodePar,
assign_values_to_leaves_nodePar - now ignores “Inf” also
when it is a character by adding as.numeric (and not only if it is
numeric!) (this might be a problem if someone would try to update a
label with the name “Inf”).dendextend_options
functions to it.branches_attr_by_labels between two
files.assign_values_to_branches_edgePar - make sure it deals
with Inf and “Inf”.as.dendrogram.pvclust - extract the hclust from a
pvclust object, and turns it into a dendrogram.hc2axes - imported from pvclust, needed for
text.pvclusttext.pvclust - imported from pvclust, adds text to a
dend plot of a pvclust resultpvclust_show_signif - Shows the significant branches in
a dendrogram, based on a pvclust objectpvclust_show_signif_gradient - Shows the gradient of
significance of branches in a dendrogram, based on a pvclust objectassign_values_to_leaves_nodePar,
assign_values_to_nodes_nodePar,
assign_values_to_branches_edgePar - If the value has
Inf (instead of NA!) then the value will not be
changed.assign_values_to_nodes_nodePar - Assign values to
nodePar of dendrogram’s nodesassign_values_to_leaves_nodePar - If the value has NA
then the value in edgePar will not be changed.branches_attr_by_clusters - This function was designed
to enable the manipulation (mainly coloring) of branches, based on the
results from the cutreeDynamic function (from the {dynamicTreeCut}
package).which_leaf - Which node is a leaf?na_locf - Fill Last Observation Carried Forwardcolored_bars - change the order of colors and dend, and
allowing for dend to be missing. (also some other doc
modifications)branches_attr_by_labels - change the order of some
parameters (based on how much I expect users to use each of them.)assign_values_to_branches_edgePar - allow the option to
skip leavesnoded_with_condition - Find which nodes satisfies a
conditionbranches_attr_by_labels - Change col/lwd/lty of
branches matching labels conditionrect.dendrogram - adding paramters for creating text
under the clusters, as well as make it easier to plot lines on the rect
(density = 7). props to skullkey for his help.set.dendrogram - added new options:
by_labels_branches_col, by_labels_branches_lwd,
by_labels_branches_ltyorder.hclust - Ordering of the Leaves in a hclust
Dendrogramrect.dendrogram - just like rect.hclust,
plus: works for dendrograms, passes ... to rect for lwd lty
etc, now has an horiz parameter!identify.dendrogram - like
identify.hclust: reads the position of the graphics pointer
when the (first) mouse button is pressed. It then cuts the tree at the
vertical position of the pointer and highlights the cluster containing
the horizontal position of the pointer. Optionally a function is applied
to the index of data points contained in the cluster.rect.dendrogram.R
add functions to be called set.
Reason: both are short names (important for chaining), both are not used
in base R. “add” is used in magrittr (not good long term), and “set”
sounds better English wise (we are setting labels color, more than
adding it…).dendlist - a function which creates a list of
dendrogram of the new “dendlist” class.
tanglegram.dendlistentanglement.dendlistis.dendlist - to check that an object is a
dendlistas.dendlist - to turn a list to a dendlistplot.dendlist - it is basically a wrapper to
tanglegram.click_rotate - interactively rotate a tree (thanks to
Andrej-Nikolai Spiess)untangle - a master function to control all untangle
functions (making it much easier to navigate this feature, as well as
use it through %>% piping)untangle_DendSer - a new untangle function (this time,
only for dendlist), for leverging the serialization package for some
more heuristics (based on the functions rotate_DendSer and
DendSer.dendrogram).add.dendrogram - a new master function to allow various
updating of dendrogram objects. It includes options for: labels,
labels_colors, labels_cex, branches_color, hang, leaves_pch, leaves_cex,
leaves_col, branches_k_color, branches_col, branches_lwd, branches_lty,
clear_branches, clear_leavesadd.dendlist - a wrapper to add.dendrogram.colored_bars - adding colored bars underneath a
dendrogram plot.untangle functions will return
a dendlist (and also that untangle_step_rotate_2side will
be able to work with the new untangle_step_rotate_1side output)labels_colors<- - now has a default behavior if
value is missing. Also made sure it is more robust (for cases with
partiel attr in nodePar)color_branches - now has a default behavior if k is
missing.assign_values_to_branches_edgePar - value can now be
different than 1 (it now also has a recycle option for the value)is.dendrogram more.tanglegram - now preserve and restore previous par
options (will no longer have a tiny plot in the left corner, when using
a simple plot after tanglegram)tanglegram.dendlistFILE CHANGES: * Bk-method.r file added.
cor_bakers_gamma
sample.dendrogram
rank_order.dendrogram - for fixing leaves value order.
duplicate_leaf - for sample.dendrogram
sample.dendrogram - for bootstraping trees when the original data table is missing.
sort_dist_mat
cor_cophenetic
FILE CHANGES: * sample.dendrogram.r file added.
tanglegram - major addition!
plot_horiz.dendrogram - Plotting a left-tip-adjusted horizontal dendrogram
remove_leaves_nodePar
assign_values_to_branches_edgePar
remove_branches_edgePar
match_order_by_labels
match_order_dendrogram_by_old_order - like match_order_by_labels, but faster
entanglement
(including tests and documentation) * is.natural.number * cutree_1h.dendrogram - like cutree, but only for 1 height value. * fix_members_attr.dendrogram - just to validate that prune works o.k. * hang.dendrogram - hangs a dendrogram leaves (also allows for a rotated hanged dendrogram), works also for non-binary trees. * nnodes - count the number of nodes in a tree * as.dendrogram.phylo - based on as.hclust. * get_nodes_attr - allows easy access to attributes of branches and leaves * get_branches_heights * fix_members_attr.dendrogram * heights_per_k.dendrogram - get the heights for a tree that will yield each k cluster. * is.hclust * is.dendrogram * is.phylo * fac2num * as.phylo.dendrogram - based on as.hclust.
cutree_1k.dendrogram - like cutree, but only for 1 k (number of clusters) value.
cutree.dendrogram - like cutree but for dendrograms (and it is also vectorized)
cutree.hclust - like cutree but for hclust
cutree.phylo - like cutree but for phylo
sort_levels_values - make the resulting clusters from cutree to be ordered from left to right
cutree - with S3 methods for dendrogram/hclust/phylo
color_branches - color a tree branches based on its clusters. This is a modified version of the color_clusters function from jefferis’s dendroextra package. It extends it by using my own version of cutree.dendrogram - allowing the function to work for trees that hclust can not handle (unrooted and non-ultrametric trees). Also, it allows REPEATED cluster color assignments to branches on to the same tree. Something which the original function was not able to handle. It also handles extreme cases, such as when the labels of a tree are integers.
color_labels - just like color_branches, but for labels.
assign_values_to_leaves_nodePar - allows for complex manipulation of dendrogram’s leaves parameters.
* Includes skeletons for some functions that will be added in the future.