tanglegram | Plot tanglegrams from two dendrograms | Data Visualization library

by schlegelp Python Version: 0.2.0 License: GPL-3.0

X-Ray Key Features Code Snippets(1)Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | tanglegram Summary

tanglegram is a Python library typically used in Analytics, Data Visualization applications. tanglegram has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install tanglegram' or download it from GitHub, PyPI.

Python wrapper for scipy and matplotlib to plot tanglegrams from two dendrograms

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Quality

Security

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Support

tanglegram has a low active ecosystem.

It has 16 star(s) with 4 fork(s). There are 4 watchers for this library.

It had no major release in the last 12 months.

There are 8 open issues and 4 have been closed. On average issues are closed in 13 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of tanglegram is 0.2.0

Quality

tanglegram has no bugs reported.

Security

tanglegram has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

tanglegram is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

tanglegram releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

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tanglegram Key Features

No Key Features are available at this moment for tanglegram.

tanglegram Examples and Code Snippets

Quickstart

Python

Lines of Code : 23

License : Strong Copyleft (GPL-3.0)

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import tanglegram as tg
import matplotlib.pyplot as plt
import pandas as pd

# Generate two distance matrices and just switch labels in one
labelsA= ['A', 'B', 'C', 'D']
labelsB= ['B', 'A', 'C', 'D']
data = [[ 0,  .1,  .4, .3],
        [.1,   0,  .5,

Community Discussions

Trending Discussions on tanglegram

How can I create a large tanglegram in R that is readable and can be saved

How to perform hierarchical clustering with predifined clusters/classes?

Coloring lines in tanglegram based on position of nodes

Combine dendrogram with bipartite graphs in R (tanglegram)

QUESTION

How can I create a large tanglegram in R that is readable and can be saved

Asked 2020-Nov-21 at 13:52

I am using cophyloplot to create a tanglegram of two phylogenetic trees. The method works well with small trees but as the trees get larger the output image remains the same size and I can't find a way to expand it.

Below is the code for a small tree that works fine (basically same as example at: https://www.rdocumentation.org/packages/ape/versions/5.4-1/topics/cophyloplot):

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ANSWER

Answered 2020-Nov-21 at 13:52

The tanglegram function comes with many options to improve the output of the image you get (especially the arguments lab.cex and margin_inner). Probably the biggest factor though is external to tanglegram and is the size of your graphic device (via dev.new), so playing with the width and height there would probably solve most of the issue

Here is a simple self contained code that shows how to play with these options to get a nice output.

Source https://stackoverflow.com/questions/64881039

QUESTION

How to perform hierarchical clustering with predifined clusters/classes?

Asked 2020-Mar-30 at 18:42

I have a database I did hierarchical clustering on (with agnes()) and it worked well (I did it like here described: https://uc-r.github.io/hc_clustering. Now I want to compare manmade clusters or classes in the database with the ones that the hierarchical clustering found. I think I can do this with tanglegram(). I do not know how to generate a dendrogram/ doing hierarchical clustering when I already have groups. How can I tell R about the groups? It would be great if you could answer this question methodical. `

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ANSWER

Answered 2020-Mar-30 at 12:08

To compare the clusters visually you can use plotDendroAndColors() function from WGCNA package. The function simply displays custom color information for each object under the dendrogram.

I cannot reproduce your example (the packages you used in your code are not specified), so I am demonstrating this using a simple clustering of iris dataset:

Source https://stackoverflow.com/questions/60929910

QUESTION

Coloring lines in tanglegram based on position of nodes

Asked 2019-Jul-23 at 20:49

I am creating tanglegrams with the following code:

...

ANSWER

Answered 2019-Jul-23 at 20:49

You can construct a column in dd that checks if the line will be horizontal. Here I grouped by label and checked whether the number of unique id's is 1. Then you use that column to the color argument in the aes of the line.

Source https://stackoverflow.com/questions/57161083

QUESTION

Combine dendrogram with bipartite graphs in R (tanglegram)

Asked 2018-Oct-23 at 13:42

I am currently working on creating a tanglegram where species reared are on one side and substrate reared on is on the other side. However, I need the output to also be a tanglegram, having each side of the chart be the tips of a dendogram. I currently have phylogenies of both the species and substrates in Newick formats.

I successfully used the 'ape' package and the plot.phylo() function to generate the 2 phylogenies. I then used the following code from this post to export the order of tips:

...

ANSWER

Answered 2018-Oct-15 at 23:57

You can use the function cophylo from the phytools package:

Source https://stackoverflow.com/questions/52823323

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install tanglegram

First, get [PIP](https://pip.pypa.io/en/stable/installing/) and then run in terminal:.
[Pandas](http://pandas.pydata.org/)
[SciPy](http://www.scipy.org)
[Numpy](http://www.scipy.org)
[Matplotlib](http://www.matplotlib.org)

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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