{ "_id": "6a10437dacfb0bcc41c9df22", "Package": "dendextend", "Type": "Package", "Title": "Extending 'dendrogram' Functionality in R", "Version": "1.19.1", "Date": "2025-07-15", "Authors@R": "c(person(\"Tal\", \"Galili\", role = c(\"aut\", \"cre\", \"cph\"), email =\n\"tal.galili@gmail.com\", comment = \"https://www.r-statistics.com\"),\nperson(\"Yoav\", \"Benjamini\", email = \"ybenja@tau.ac.il\",role = \"ths\"),\nperson(\"Gavin\", \"Simpson\", role = \"ctb\"), person(\"Gregory\",\"Jefferis\", role\n= c(\"aut\", \"ctb\"), email = \"jefferis@gmail.com\",\ncomment =\"imported code from his dendroextras package\"),\nperson(\"Marco\", \"Gallotta\", role = \"ctb\", comment =\n\"a.k.a: marcog\") , person(\"Johan\", \"Renaudie\", role = \"ctb\", comment =\n\"https://github.com/plannapus\"), person(\"The R Core Team\", role = \"ctb\",\ncomment = \"Thanks for the Infastructure, and code in the examples\"),\nperson(\"Kurt\", \"Hornik\", role = \"ctb\"), person(\"Uwe\", \"Ligges\",\nrole = \"ctb\"), person(\"Andrej-Nikolai\", \"Spiess\", role = \"ctb\"),\nperson(\"Steve\", \"Horvath\",email = \"SHorvath@mednet.ucla.edu\", role =\n\"ctb\"), person(\"Peter\", \"Langfelder\",email = \"Peter.Langfelder@gmail.com\",\nrole = \"ctb\"), person(\"skullkey\", role = \"ctb\"), person(\"Mark\",\n\"Van Der Loo\", email = \"mark.vanderloo@gmail.com\", comment =\n\"https://github.com/markvanderloo d3dendrogram\", role = \"ctb\"),\nperson(\"Andrie\",\n\"de Vries\", email = \"apdevries@gmail.com\", comment =\n\"ggdendro author\", role = \"ctb\"),\nperson(\"Zuguang\",\n\"Gu\", email = \"z.gu@dkfz-heidelberg.de\", comment =\n\"circlize author\", role = \"ctb\"),\nperson(\"Cath\", comment =\n\"https://github.com/CathG\", role = \"ctb\"), person(\"John\",\n\"Ma\", comment =\n\"https://github.com/JohnMCMa\", role = \"ctb\"), person(\"Krzysiek\",\n\"G\", comment =\n\"https://github.com/storaged\", role = \"ctb\"), person(\"Manuela\",\n\"Hummel\", email = \"m.hummel@dkfz.de\", comment =\n\"https://github.com/hummelma\", role = \"ctb\"),\nperson(\"Chase\",\n\"Clark\", comment =\n\"https://github.com/chasemc\", role = \"ctb\"),\nperson(\"Lucas\",\n\"Graybuck\", comment =\n\"https://github.com/hypercompetent\", role = \"ctb\"),\nperson(\"jdetribol\", comment =\n\"https://github.com/jdetribol\", role = \"ctb\"),\nperson(\"Ben\", \"Ho\", role = \"ctb\", email = \"ben.ho@sickkids.ca\", comment = \"https://github.com/SplitInf\"),\nperson(\"Samuel\", \"Perreault\", role = \"ctb\", email = \"samuel.perreault.3@ulaval.ca\", comment = \"https://github.com/samperochkin\"),\nperson(\"Christian\", \"Hennig\", role = \"ctb\", email = \"c.hennig@ucl.ac.uk\", comment = \"http://www.homepages.ucl.ac.uk/~ucakche/\"),\nperson(\"David\", \"Bradley\", role = \"ctb\", comment = \"https://github.com/DBradley27\"),\nperson(\"Houyun\", \"Huang\", role = \"ctb\", email = 'houyunhuang@163.com', comment = \"https://github.com/houyunhuang\"),\nperson(\"Patrick\", \"Schupp\", role = \"ctb\", email = 'pschupp@sonic.net', comment = \"https://github.com/pschupp\"),\nperson(\"Alec\", \"Buetow\", role = \"ctb\", email = 'alecbuetow@gmail.com', comment = \"https://github.com/alecbuetow\")\n)", "Description": "Offers a set of functions for extending 'dendrogram'\nobjects in R, letting you visualize and compare trees of\n'hierarchical clusterings'. You can (1) Adjust a tree's\ngraphical parameters - the color, size, type, etc of its\nbranches, nodes and labels. (2) Visually and statistically\ncompare different 'dendrograms' to one another.", "VignetteBuilder": "knitr", "LazyData": "true", "License": "GPL-2 | GPL-3", "URL": "https://talgalili.github.io/dendextend/,\nhttps://github.com/talgalili/dendextend/,\nhttps://cran.r-project.org/package=dendextend,\nhttps://www.r-statistics.com/tag/dendextend/,\nhttps://doi.org/10.1093/bioinformatics/btv428", "BugReports": "https://github.com/talgalili/dendextend/issues", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2025-07-15 03:37:53 UTC", "RemoteUrl": "https://github.com/talgalili/dendextend", "RemoteRef": "HEAD", "RemoteSha": "0af62aaee571042d82012e444842700890526f73", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 06:58:52 UTC", "User": "root" }, "Author": "Tal Galili [aut, cre, cph] (https://www.r-statistics.com),\nYoav Benjamini [ths],\nGavin Simpson [ctb],\nGregory Jefferis [aut, ctb] (imported code from his dendroextras\npackage),\nMarco Gallotta [ctb] (a.k.a: marcog),\nJohan Renaudie [ctb] (https://github.com/plannapus),\nThe R Core Team [ctb] (Thanks for the Infastructure, and code in the\nexamples),\nKurt Hornik [ctb],\nUwe Ligges [ctb],\nAndrej-Nikolai Spiess [ctb],\nSteve Horvath [ctb],\nPeter Langfelder [ctb],\nskullkey [ctb],\nMark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),\nAndrie de Vries [ctb] (ggdendro author),\nZuguang Gu [ctb] (circlize author),\nCath [ctb] (https://github.com/CathG),\nJohn Ma [ctb] (https://github.com/JohnMCMa),\nKrzysiek G [ctb] (https://github.com/storaged),\nManuela Hummel [ctb] (https://github.com/hummelma),\nChase Clark [ctb] (https://github.com/chasemc),\nLucas Graybuck [ctb] (https://github.com/hypercompetent),\njdetribol [ctb] (https://github.com/jdetribol),\nBen Ho [ctb] (https://github.com/SplitInf),\nSamuel Perreault [ctb] (https://github.com/samperochkin),\nChristian Hennig [ctb] 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"page": "assign_dendextend_options", "title": "Populates dendextend functions into dendextend_options", "topics": [ "assign_dendextend_options" ] }, { "page": "assign_values_to_branches_edgePar", "title": "Assign values to edgePar of dendrogram's branches", "topics": [ "assign_values_to_branches_edgePar" ] }, { "page": "assign_values_to_leaves_edgePar", "title": "Assign values to edgePar of dendrogram's leaves", "topics": [ "assign_values_to_leaves_edgePar" ] }, { "page": "assign_values_to_leaves_nodePar", "title": "Assign values to nodePar of dendrogram's leaves", "topics": [ "assign_values_to_leaves_nodePar" ] }, { "page": "assign_values_to_nodes_nodePar", "title": "Assign values to nodePar of dendrogram's nodes", "topics": [ "assign_values_to_nodes_nodePar" ] }, { "page": "bakers_gamma_for_2_k_matrix", "title": "Bakers Gamma for two k matrices", "topics": [ "bakers_gamma_for_2_k_matrix" ] }, { "page": "Bk", "title": "Bk - Calculating Fowlkes-Mallows Index for two dendrogram", "topics": [ "Bk" ] }, { "page": "Bk_permutations", "title": "Bk permutation - Calculating Fowlkes-Mallows Index for two dendrogram", "topics": [ "Bk_permutations" ] }, { "page": "Bk_plot", "title": "Bk plot - ploting the Fowlkes-Mallows Index of two dendrogram for various k's", "topics": [ "Bk_plot" ] }, { "page": "branches_attr_by_clusters", "title": "Change col/lwd/lty of branches based on clusters", "topics": [ "branches_attr_by_clusters" ] }, { "page": "branches_attr_by_labels", "title": "Change col/lwd/lty of branches matching labels condition", "topics": [ "branches_attr_by_labels" ] }, { "page": "branches_attr_by_lists", "title": "Change col/lwd/lty of branches from the root down to clusters defined by list of labels of respective members", "topics": [ "branches_attr_by_lists" ] }, { "page": "circlize_dendrogram", "title": "Plot a circlized dendrograms", "topics": [ "circlize_dendrogram" ] }, { "page": "click_rotate", "title": "Interactively rotate a tree object", "topics": [ "click_rotate", "click_rotate.default", "click_rotate.dendrogram" ] }, { "page": "collapse_branch", "title": "Collapse branches under a tolerance level", "topics": [ "collapse_branch" ] }, { "page": "collapse_labels", "title": "Collapse a sub dendrogram of adjacent labels within a dend", "topics": [ "collapse_labels" ] }, { "page": "color_branches", "title": "Color tree's branches according to sub-clusters", "topics": [ "branches_color", "color_branches", "colour_branches" ] }, { "page": "color_labels", "title": "Color dend's labels according to sub-clusters", "topics": [ "color_labels", "colour_labels" ] }, { "page": "color_unique_labels", "title": "Color unique labels in a dendrogram", "topics": [ "color_unique_labels" ] }, { "page": "colored_bars", "title": "Add colored bars to a dendrogram", "topics": [ "colored_bars" ] }, { "page": "colored_dots", "title": "Add colored dots beside a dendrogram", "topics": [ "colored_dots" ] }, { "page": "common_subtrees_clusters", "title": "Find clusters of common subtrees", "topics": [ "common_subtrees_clusters" ] }, { "page": "cor_bakers_gamma", "title": "Baker's Gamma correlation coefficient", "topics": [ "cor_bakers_gamma", "cor_bakers_gamma.default", "cor_bakers_gamma.dendlist", "cor_bakers_gamma.dendrogram", "cor_bakers_gamma.hclust" ] }, { "page": "cor_common_nodes", "title": "Proportion of commong nodes between two trees", "topics": [ "cor_common_nodes" ] }, { "page": "cor_cophenetic", "title": "Cophenetic correlation between two trees", "topics": [ "cor_cophenetic", "cor_cophenetic.default", "cor_cophenetic.dendlist" ] }, { "page": "cor_FM_index", "title": "Correlation of FM_index for some k", "topics": [ "cor_FM_index" ] }, { "page": "cor.dendlist", "title": "Correlation matrix between a list of trees.", "topics": [ "cor.dendlist" ] }, { "page": "count_terminal_nodes", "title": "Counts the number of terminal nodes (merging 0 nodes!)", "topics": [ "count_terminal_nodes" ] }, { "page": "cut_lower_fun", "title": "Cut a dendrogram - and run a function on the output", "topics": [ "cut_lower_fun", "dendextend_cut_lower_fun" ] }, { "page": "cutree-methods", "title": "Cut a Tree (Dendrogram/hclust/phylo) into Groups of Data", "topics": [ "cutree", "cutree.agnes", "cutree.default", "cutree.dendrogram", "cutree.diana", "cutree.hclust", "cutree.phylo" ] }, { "page": "cutree_1h.dendrogram", "title": "cutree for dendrogram (by 1 height only!)", "topics": [ "cutree_1h.dendrogram" ] }, { "page": "cutree_1k.dendrogram", "title": "cutree for dendrogram (by 1 k value only!)", "topics": [ "cutree_1k.dendrogram" ] }, { "page": "dend_diff", "title": "Plots two trees side by side, highlighting edges unique to each tree in red.", "topics": [ "dend_diff", "dend_diff.dendlist", "dend_diff.dendrogram" ] }, { "page": "find_dend", "title": "Finds a \"good\" dendrogram for a dist", "topics": [ "dend_expend", "find_dend" ] }, { "page": "dendextend_options", "title": "Access to dendextend_options", "topics": [ "dendextend_options" ] }, { "page": "dendlist", "title": "Creating a dendlist object from several dendrograms", "topics": [ "dendlist", "plot.dendlist" ] }, { "page": "DendSer.dendrogram", "title": "Tries to run DendSer on a dendrogram", "topics": [ "DendSer.dendrogram" ] }, { "page": "dist_long", "title": "Turns a dist object to a \"long\" table", "topics": [ "dist_long" ] }, { "page": "dist.dendlist", "title": "Topological Distances Between Two dendrograms", "topics": [ "dist.dendlist" ] }, { "page": "distinct_edges", "title": "Finds distinct edges in one tree compared to another", "topics": [ "distinct_edges" ] }, { "page": "duplicate_leaf", "title": "Duplicate a leaf X times", "topics": [ "duplicate_leaf" ] }, { "page": "entanglement", "title": "Measures entanglement between two trees", "topics": [ "entanglement", "entanglement.dendlist", "entanglement.dendrogram", "entanglement.hclust", "entanglement.phylo" ] }, { "page": "fac2num", "title": "Turns a factor into a number", "topics": [ "fac2num" ] }, { "page": "find_dendrogram", "title": "Search for the sub-dendrogram structure composed of selected labels", "topics": [ "find_dendrogram" ] }, { "page": "find_k", "title": "Find the (estimated) number of clusters for a dendrogram using average silhouette width", "topics": [ "find_k", "plot.find_k" ] }, { "page": "fix_members_attr.dendrogram", "title": "Fix members attr in a dendrogram", "topics": [ "fix_members_attr.dendrogram" ] }, { "page": "flatten.dendrogram", "title": "Flatten the branches of a dendrogram's root", "topics": [ "flatten.dendrogram" ] }, { "page": "flip_leaves", "title": "Flip leaves", "topics": [ "flip_leaves" ] }, { "page": "FM_index", "title": "Calculating Fowlkes-Mallows Index", "topics": [ "FM_index" ] }, { "page": "FM_index_permutation", "title": "Calculating Fowlkes-Mallows Index under H0", "topics": [ "FM_index_permutation" ] }, { "page": "FM_index_R", "title": "Calculating Fowlkes-Mallows index in R", "topics": [ "FM_index_R" ] }, { "page": "get_branches_heights", "title": "Get height attributes from a dendrogram", "topics": [ "get_branches_heights" ] }, { "page": "get_childrens_heights", "title": "Get height attributes from a dendrogram's children", "topics": [ "get_childrens_heights" ] }, { "page": "get_leaves_attr", "title": "Get/set attributes of dendrogram's leaves", "topics": [ "get_leaves_attr" ] }, { "page": "get_leaves_branches_attr", "title": "Get an attribute of the branches of a dendrogram's leaves", "topics": [ "get_leaves_branches_attr" ] }, { "page": "get_leaves_branches_col", "title": "Get the colors of the branches of a dendrogram's leaves", "topics": [ "get_leaves_branches_col" ] }, { "page": "get_leaves_edgePar", "title": "Get edgePar of dendrogram's leaves", "topics": [ "get_leaves_edgePar" ] }, { "page": "get_leaves_nodePar", "title": "Get nodePar of dendrogram's leaves", "topics": [ "get_leaves_nodePar" ] }, { "page": "get_nodes_attr", "title": "Get attributes of dendrogram's nodes", "topics": [ "get_nodes_attr" ] }, { "page": "get_nodes_xy", "title": "Get the x-y coordinates of a dendrogram's nodes", "topics": [ "get_nodes_xy" ] }, { "page": "get_root_branches_attr", "title": "get attributes from the dendrogram's root(!) branches", "topics": [ "get_root_branches_attr" ] }, { "page": "get_subdendrograms", "title": "Extract a list of _k_ subdendrograms from a given dendrogram object", "topics": [ "get_subdendrograms" ] }, { "page": "ggdend", "title": "Creates dendrogram plot using ggplot.", "topics": [ "as.ggdend", "as.ggdend.dendrogram", "ggdend", "ggplot.dendrogram", "ggplot.ggdend", "prepare.ggdend", "print.ggdend" ] }, { "page": "hang.dendrogram", "title": "Hang dendrogram leaves", "topics": [ "hang.dendrogram" ] }, { "page": "has_component_in_attribute", "title": "Does a dendrogram has an edgePar/nodePar component?", "topics": [ "has_component_in_attribute", "has_edgePar", "has_nodePar" ] }, { "page": "heights_per_k.dendrogram", "title": "Which height will result in which k for a dendrogram", "topics": [ "dendextend_heights_per_k.dendrogram", "heights_per_k.dendrogram" ] }, { "page": "highlight_branches", "title": "Highlight a dendrogram's branches heights via color and line-width", "topics": [ "highlight_branches", "highlight_branches_col", "highlight_branches_lwd" ] }, { "page": "highlight_distinct_edges", "title": "Highlight distint edges in a tree (compared to another one)", "topics": [ "highlight_distinct_edges", "highlight_distinct_edges.dendlist", "highlight_distinct_edges.dendrogram" ] }, { "page": "identify.dendrogram", "title": "Identify Clusters in a Dendrogram (not hclust)", "topics": [ "identify.dendrogram" ] }, { "page": "intersect_trees", "title": "Intersect trees", "topics": [ "intersect_trees" ] }, { "page": "is_null_list", "title": "Checks if the value is and empty list()", "topics": [ "is_null_list" ] }, { "page": "is_some_class", "title": "Is the object of some class", "topics": [ "is.dendlist", "is.dendrogram", "is.dist", "is.hclust", "is.phylo", "is_some_class" ] }, { "page": "is.natural.number", "title": "Check if numbers are natural", "topics": [ "is.natural.number" ] }, { "page": "khan", "title": "Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.", "topics": [ "khan" ] }, { "page": "labels_cex", "title": "Retrieve/assign cex to the labels of a dendrogram", "topics": [ "labels_cex", "labels_cex<-" ] }, { "page": "labels_colors", "title": "Retrieve/assign colors to the labels of a dendrogram", "topics": [ "labels_col", "labels_colors", "labels_colors<-" ] }, { "page": "labels-assign", "title": "\"label\" assignment operator", "topics": [ "labels.hclust", "labels.phylo", "labels<-", "labels<-.default", "labels<-.dendrogram", "labels<-.hclust", "labels<-.phylo" ] }, { "page": "ladderize", "title": "Ladderize a Tree", "topics": [ "ladderize", "ladderize.dendlist", "ladderize.dendrogram", "ladderize.phylo" ] }, { "page": "leaf_Colors", "title": "Return the leaf Colors of a dendrogram", "topics": [ "leaf_Colors", "leaf_colors" ] }, { "page": "lowest_common_branch", "title": "Find lowest common branch were the two items are shared", "topics": [ "lowest_common_branch" ] }, { "page": "match_order_by_labels", "title": "Adjust the order of one dendrogram based on another (using labels)", "topics": [ "match_order_by_labels" ] }, { "page": "match_order_dendrogram_by_old_order", "title": "Adjust the order of one dendrogram based on another (using order)", "topics": [ "match_order_dendrogram_by_old_order" ] }, { "page": "depth", "title": "Find minimum/maximum depth of a dendrogram", "topics": [ "max_depth", "min_depth" ] }, { "page": "na_locf", "title": "Last Observation Carried Forward", "topics": [ "na_locf" ] }, { "page": "nleaves", "title": "Counts the number of leaves in a tree", "topics": [ "nleaves", "nleaves.default", "nleaves.dendlist", "nleaves.dendrogram", "nleaves.hclust", "nleaves.phylo" ] }, { "page": "nnodes", "title": "Counts the number of nodes (Vertices) in a tree", "topics": [ "nnodes", "nnodes.default", "nnodes.dendrogram", "nnodes.hclust", "nnodes.phylo" ] }, { "page": "noded_with_condition", "title": "Find which nodes satisfies a condition", "topics": [ "noded_with_condition" ] }, { "page": "order.dendrogram-assign", "title": "order.dendrogram<- assignment operator", "topics": [ "order.dendrogram<-" ] }, { "page": "order.hclust", "title": "Ordering of the Leaves in a hclust Dendrogram", "topics": [ "order.hclust" ] }, { "page": "partition_leaves", "title": "A list with labels for each subtree (edge)", "topics": [ "partition_leaves" ] }, { "page": "plot_horiz.dendrogram", "title": "Plotting a left-tip-adjusted horizontal dendrogram", "topics": [ "plot_horiz.dendrogram" ] }, { "page": "prune", "title": "Prunes a tree (using leaves' labels)", "topics": [ "prune", "prune.default", "prune.dendrogram", "prune.hclust", "prune.phylo", "prune.rpart" ] }, { "page": "prune_common_subtrees.dendlist", "title": "Prune trees to their common subtrees", "topics": [ "prune_common_subtrees.dendlist" ] }, { "page": "prune_leaf", "title": "Trims one leaf from a dendrogram", "topics": [ "prune_leaf" ] }, { "page": "pvclust_edges", "title": "Get Pvclust Edges Information", "topics": [ "pvclust_edges" ] }, { "page": "pvclust_show_signif", "title": "The significant branches in a dendrogram, based on a pvclust object", "topics": [ "pvclust_show_signif" ] }, { "page": "pvclust_show_signif_gradient", "title": "Significance gradient of branches in a dendrogram (via pvclust)", "topics": [ "pvclust_show_signif_gradient" ] }, { "page": "pvrect2", "title": "Draw Rectangles Around a Dendrogram's Clusters with High/Low P-values", "topics": [ "pvrect2" ] }, { "page": "raise.dendrogram", "title": "Raise the height of a dendrogram tree", "topics": [ "raise.dendrogram" ] }, { "page": "rank_branches", "title": "Rank branches' heights", "topics": [ "rank_branches" ] }, { "page": "rank_order.dendrogram", "title": "Fix rank of leaves order values in a dendrogram", "topics": [ "rank_order.dendrogram" ] }, { "page": "rank_values_with_clusters", "title": "Rank a vector based on clusters", "topics": [ "rank_values_with_clusters" ] }, { "page": "rect.dendrogram", "title": "Draw Rectangles Around a Dendrogram's Clusters", "topics": [ "rect.dendrogram" ] }, { "page": "reindex_dend", "title": "Reindexing a pruned dendrogram", "topics": [ "reindex_dend" ] }, { "page": "remove_branches_edgePar", "title": "Remove all edgePar values from a dendrogram's branches", "topics": [ "remove_branches_edgePar" ] }, { "page": "remove_leaves_nodePar", "title": "Remove all nodePar values from a dendrogram's leaves", "topics": [ "remove_leaves_nodePar" ] }, { "page": "remove_nodes_nodePar", "title": "Remove all nodePar values from a dendrogram's nodes", "topics": [ "remove_nodes_nodePar" ] }, { "page": "rllply", "title": "recursivly apply a function on a list", "topics": [ "rllply" ] }, { "page": "rotate", "title": "Rotate a tree object", "topics": [ "rev.hclust", "rotate", "rotate.default", "rotate.dendrogram", "rotate.hclust", "rotate.phylo", "sort.dendlist", "sort.dendrogram", "sort.hclust" ] }, { "page": "rotate_DendSer", "title": "Rotates dend based on DendSer", "topics": [ "rotate_DendSer" ] }, { "page": "sample.dendrogram", "title": "Sample a tree", "topics": [ "sample.dendrogram" ] }, { "page": "seriate_dendrogram", "title": "Rotates a dendrogram based on a seriation of a distance matrix", "topics": [ "seriate_dendrogram" ] }, { "page": "set", "title": "Set (/update) features to a dendrogram", "topics": [ "set", "set.data.table", "set.dendlist", "set.dendrogram" ] }, { "page": "set_labels", "title": "Set/place new labels in a dendrogram", "topics": [ "place_labels", "set_labels" ] }, { "page": "shuffle", "title": "Random rotation of trees", "topics": [ "shuffle", "shuffle.default", "shuffle.dendlist", "shuffle.dendrogram", "shuffle.hclust", "shuffle.phylo" ] }, { "page": "sort_2_clusters_vectors", "title": "Sorts two clusters vector by their names", "topics": [ "sort_2_clusters_vectors" ] }, { "page": "sort_dist_mat", "title": "Sorts a distance matrix by rows and columns names", "topics": [ "sort_dist_mat" ] }, { "page": "sort_levels_values", "title": "Sort the values level in a vector", "topics": [ "sort_levels_values" ] }, { "page": "tanglegram", "title": "Tanglegram plot", "topics": [ "dendbackback", "tanglegram", "tanglegram.default", "tanglegram.dendlist", "tanglegram.dendrogram", "tanglegram.hclust", "tanglegram.phylo" ] }, { "page": "theme_dendro", "title": "Creates completely blank theme in ggplot", "topics": [ "theme_dendro" ] }, { "page": "unbranch", "title": "unbranch trees", "topics": [ "unbranch", "unbranch.default", "unbranch.dendrogram", "unbranch.hclust", "unbranch.phylo" ] }, { "page": "unclass_dend", "title": "unclass an entire dendrogram tree", "topics": [ "unclass_dend" ] }, { "page": "untangle", "title": "untangle dendrograms", "topics": [ "untangle", "untangle.default", "untangle.dendlist", "untangle.dendrogram", "untangle_labels" ] }, { "page": "untangle_DendSer", "title": "Tries to run DendSer on a dendrogram", "topics": [ "untangle_DendSer" ] }, { "page": "untangle_random_search", "title": "Untangle - random search", "topics": [ "untangle_random_search" ] }, { "page": "untangle_step_rotate_1side", "title": "Stepwise untangle one tree compared to another", "topics": [ "untangle_step_rotate_1side" ] }, { "page": "untangle_step_rotate_2side", "title": "Stepwise untangle two trees one at a time", "topics": [ "untangle_step_rotate_2side" ] }, { "page": "untangle_step_rotate_both_side", "title": "Stepwise untangle two trees at the same time", "topics": [ "untangle_step_rotate_both_side" ] }, { "page": "which_leaf", "title": "Which node is a leaf?", "topics": [ "which_leaf" ] }, { "page": "which_node", "title": "Which node id is common to a group of labels", "topics": [ "which_node" ] } ], "_readme": "https://github.com/talgalili/dendextend/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "Quick_Introduction.Rmd", "filename": "Quick_Introduction.html", "title": "Quick Introduction", "author": "Tal Galili", "engine": "knitr::rmarkdown", "headings": [ "Start" ], "created": "2015-06-28 18:05:03", "modified": "2020-08-24 18:02:13", "commits": 6 }, { "source": "FAQ.Rmd", "filename": "FAQ.html", "title": "Frequently asked questions", "author": "Tal Galili", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "How to colour the labels of a dendrogram by an additional factor variable", "How to color a dendrogram's labels according to defined groups? (in R)", "How to color a dendrogram's branches/labels based on cluster (i.e.: cutree result)", "Change dendrogram's labels", "Larger font for leaves in a dendrogram", "How to view attributes of a dendrogram", "How to color the branches in heatmap.2?", "For package developers - how to call imported calls from dendextend 0.18.3?", "How to plot a fan (Polar) Dendrogram in R?", "A way to calculate lowest value of h in cut that produces groupings of a given minimum size?", "Coloring dendrogram's end branches (or leaves) based on column number of data frame in R", "Color side bar dendrogram plot", "Plot a \"mirror\" (labels on the left) horizontal dendrogram" ], "created": "2015-05-23 23:05:39", "modified": "2022-07-03 18:48:54", "commits": 17 }, { "source": "Cluster_Analysis.Rmd", "filename": "Cluster_Analysis.html", "title": "Hierarchical cluster analysis on famous data sets - enhanced with the dendextend package", "author": "Tal Galili", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "iris - Edgar Anderson's Iris Data", "Background", "The 3 clusters from the \"complete\" method vs the real species category", "Similarity/difference between various clustering algorithms", "Clustering prediction of the 3 species classes", "Conclusion", "khan - Microarray gene expression data set from Khan et al., 2001. Subset of 306 genes.", "Comparing the train vs test dendrograms", "votes.repub - Votes for Republican Candidate in Presidential Elections", "Heatmap", "animals - Attributes of Animals" ], "created": "2015-05-23 15:18:12", "modified": "2022-07-03 19:13:17", "commits": 21 }, { "source": "dendextend.Rmd", "filename": "dendextend.html", "title": "Introduction to dendextend", "author": "Tal Galili", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Acknowledgement", "Chaining", "A dendrogram is a nested list of lists with attributes", "Installation", "How to explore a dendrogram's parameters", "Taking a first look at a dendrogram", "Getting nodes attributes in a depth-first search", "How to change a dendrogram", "The \"set\" function", "Two simple trees to play with", "Setting a dendrogram's labels", "Setting a dendrogram's nodes/leaves (points)", "Setting a dendrogram's branches", "Adjusting all branches", "Coloring branches based on clustering", "Adjusting branches based on labels", "Highlighting branches' different heights using line width and color", "Changing a dendrogram's structure", "Rotation", "Unbranching", "Pruning", "Collapse branches", "Adding extra bars and rectangles", "Adding colored rectangles", "Adding colored bars", "ggplot2 integration", "Enhancing other packages", "DendSer", "gplots", "NMF", "heatmaply", "dynamicTreeCut", "pvclust", "circlize", "Comparing two dendrograms", "dendlist", "dend_diff", "tanglegram", "Correlation measures", "Global Comparison of two (or more) dendrograms", "Distance matrix using dist.dendlist", "Correlation matrix using cor.dendlist", "Baker's Gamma Index", "Cophenetic correlation", "The Fowlkes-Mallows Index and the Bk plot", "The Fowlkes-Mallows Index", "The Bk plot", "Session info" ], "created": "2019-07-17 20:15:15", "modified": "2023-03-25 18:16:15", "commits": 16 } ], "_score": 16.814426093207423, "_indexed": false, "_nocasepkg": "dendextend", "_universes": [ "phylotastic" ], "_indexurl": "https://talgalili.r-universe.dev/dendextend", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.1", "date": "2026-05-11T07:01:50.000Z", "distro": "noble", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "1f04bc3f5bd3e9b9d5a73a99bc8514ce12e8aa192df239a8deaee561919d668e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" }, { "r": "4.6.0", "os": "linux", "version": "1.19.1", "date": "2026-05-11T07:02:10.000Z", "distro": "noble", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "49ec0b441f8c048008c9cb9f97d657657728eb2dd356d1804a38e2e53b7dbc20", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" }, { "r": "4.5.3", "os": "mac", "version": "1.19.1", "date": "2026-05-11T07:00:51.000Z", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "78fb496d4e9bab6e56e260899a6cb11e91374e30bd83912d206ac9e3e53d7eb2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" }, { "r": "4.6.0", "os": "mac", "version": "1.19.1", "date": "2026-05-11T07:01:02.000Z", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "7bc277adb572e14c60d8d01113e852b5c150cc590b6f314957036de541d45d51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" }, { "r": "4.7.0", "os": "win", "version": "1.19.1", "date": "2026-05-11T07:00:36.000Z", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "184e8029fa18e212af391f6a2e27b263b6e14a06fa741283ad8603208a4174fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" }, { "r": "4.5.3", "os": "win", "version": "1.19.1", "date": "2026-05-11T07:00:27.000Z", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "bb9a646c442b55db1c64a078dbe5c8f28862a0a6fbd0c65667ce2d8ff2d8ecef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" }, { "r": "4.6.0", "os": "win", "version": "1.19.1", "date": "2026-05-11T07:00:33.000Z", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "056abc8257a9b166dff661d310e010939fdbf6b7232431483703e11653cf4942", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.1", "date": "2026-05-22T11:52:05.000Z", "commit": "0af62aaee571042d82012e444842700890526f73", "fileid": "7e53fc7a89ee57b1955654c352286531b48a9a121869631eb34c0efa4acca153", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25655049636" } ] }