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 |

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...

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
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