dendsort: Modular Leaf Ordering Methods for Dendrogram Nodes

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An implementation of functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization.

Author
Ryo Sakai
Date of publication
2015-12-14 12:39:17
Maintainer
Ryo Sakai <ryo@vda-lab.be>
License
GPL-2 | GPL-3
Version
0.3.3
URLs

View on CRAN

Man pages

cal_length
Recursive function to calculate the length of branches
cal_node_limit
Calculate the x coordinates given a branch of dendrogram
cal_total_length
Calculate the total length of lines to draw the dendrogram
dendsort
Sorting and reordering dendrogram nodes
dendsort-package
Modular Leaf Ordering Methods for Dendrogram Nodes
sample_tcga
Sample data matrix from the integrated pathway analysis of...
sort_average
Sorting and reordering dendrogram nodes by average distances
sort_average_r
Sorting and reordering dendrogram nodes by average distances...
sort_smallest
Sorting and reordering dendrogram nodes by the smallest value
sort_smallest_r
Sorting and reordering dendrogram nodes by the smallest value...

Files in this package

dendsort
dendsort/inst
dendsort/inst/tests
dendsort/inst/tests/test-dendsort.R
dendsort/inst/tests/test-sort_average_r.R
dendsort/inst/tests/test-sort_average.R
dendsort/inst/tests/test-sort_smallest.R
dendsort/inst/tests/test-sort_smallest_r.R
dendsort/inst/doc
dendsort/inst/doc/example_figures.R
dendsort/inst/doc/example_figures.Rmd
dendsort/inst/doc/example_figures.html
dendsort/NAMESPACE
dendsort/data
dendsort/data/sample_tcga.rda
dendsort/R
dendsort/R/sort_average.R
dendsort/R/cal_length.R
dendsort/R/dendsort-package.R
dendsort/R/cal_total_length.R
dendsort/R/dendsort.R
dendsort/R/sort_smallest.R
dendsort/R/sort_average_r.R
dendsort/R/cal_node_limit.R
dendsort/R/sort_smallest_r.R
dendsort/vignettes
dendsort/vignettes/example_figures.Rmd
dendsort/MD5
dendsort/build
dendsort/build/vignette.rds
dendsort/DESCRIPTION
dendsort/man
dendsort/man/cal_length.Rd
dendsort/man/dendsort.Rd
dendsort/man/sort_average.Rd
dendsort/man/dendsort-package.Rd
dendsort/man/sample_tcga.Rd
dendsort/man/cal_node_limit.Rd
dendsort/man/sort_smallest.Rd
dendsort/man/cal_total_length.Rd
dendsort/man/sort_smallest_r.Rd
dendsort/man/sort_average_r.Rd