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.

Install the latest version of this package by entering the following in R:

`install.packages("dendsort")`

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 |

https://bitbucket.org/vda-lab/dendsort/, http://f1000research.com/articles/3-177/v1 |

**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...

inst

inst/tests

inst/tests/test-dendsort.R
inst/tests/test-sort_average_r.R
inst/tests/test-sort_average.R
inst/tests/test-sort_smallest.R
inst/tests/test-sort_smallest_r.R
inst/doc

inst/doc/example_figures.R
inst/doc/example_figures.Rmd

inst/doc/example_figures.html

NAMESPACE

data

data/sample_tcga.rda

R

R/sort_average.R
R/cal_length.R
R/dendsort-package.R
R/cal_total_length.R
R/dendsort.R
R/sort_smallest.R
R/sort_average_r.R
R/cal_node_limit.R
R/sort_smallest_r.R
vignettes

vignettes/example_figures.Rmd

MD5

build

build/vignette.rds

DESCRIPTION

man

man/cal_length.Rd
man/dendsort.Rd
man/sort_average.Rd
man/dendsort-package.Rd
man/sample_tcga.Rd
man/cal_node_limit.Rd
man/sort_smallest.Rd
man/cal_total_length.Rd
man/sort_smallest_r.Rd
man/sort_average_r.Rd
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