dendextend: reindex_dend – R documentation

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reindex_dend

Reindexing a pruned dendrogram

Description

prune_leaf does not update leaf indices as it prune leaves. As a result, some leaves of the pruned dendrogram may have leaf indeices larger than the number of leaves in the pruned dendrogram, which may cause errors in downstream functions such as as.hclust.

This function re-indexes the leaves such that the leaf indices are no larger than the total number of leaves.

Usage

reindex_dend(dend)

Arguments

dend

dendrogram object

Value

A dendrogram object with the leaf reindexed

Examples

hc <- hclust(dist(USArrests[1:5, ]), "ave")
dend <- as.dendrogram(hc)

dend_pruned <- prune(dend, c("Alaska", "California"), reindex_dend = FALSE)

## A leave have an index larger than the number of leaves:
unlist(dend_pruned)
# [1] 4 3 1
#'
dend_pruned_reindexed <- reindex_dend(dend_pruned)

## All leaf indices are no larger than the number of leaves:
unlist(dend_pruned_reindexed)
# [1] 3 2 1

## The dendrograms are equal:
all.equal(dend_pruned, dend_pruned_reindexed)
# TRUE

dendextend

Extending 'dendrogram' Functionality in R

v1.15.1

GPL-2 | GPL-3

Authors

Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Yoav Benjamini [ths], Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Cath [ctb] (https://github.com/CathG), John Ma [ctb] (https://github.com/JohnMCMa), Krzysiek G [ctb] (https://github.com/storaged), Manuela Hummel [ctb] (https://github.com/hummelma), Chase Clark [ctb] (https://github.com/chasemc), Lucas Graybuck [ctb] (https://github.com/hypercompetent), jdetribol [ctb] (https://github.com/jdetribol), Ben Ho [ctb] (https://github.com/SplitInf), Samuel Perreault [ctb] (https://github.com/samperochkin), Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/), David Bradley [ctb] (https://github.com/DBradley27), Houyun Huang [ctb] (https://github.com/houyunhuang)

Initial release

2021-05-08