http://code.activestate.com/recipes/tags/microarray/views/2014-02-19T11:09:36-08:00ActiveState Code Recipes2012-06-26T07:29:22-07:00Nathan Salomonishttp://code.activestate.com/recipes/users/4182587/http://code.activestate.com/recipes/578175-hierarchical-clustering-heatmap-python/

<p style="color: grey"> Python recipe 578175 by <a href="/recipes/users/4182587/">Nathan Salomonis</a> (<a href="/recipes/tags/clustering/">clustering</a>, <a href="/recipes/tags/heatmap/">heatmap</a>, <a href="/recipes/tags/hierarchical/">hierarchical</a>, <a href="/recipes/tags/microarray/">microarray</a>, <a href="/recipes/tags/python/">python</a>, <a href="/recipes/tags/rnaseq/">rnaseq</a>). </p> <p>Python script that performs hierarchical clustering (scipy) on an input tab-delimited text file (command-line) along with optional column and row clustering parameters or color gradients for heatmap visualization (matplotlib). Designed particularly for transcriptome data clustering and data analyses (e.g., microarray or RNA-Seq). For example: $python hierarchical_clustering.py --i /Users/me/logfolds.txt</p>

2014-02-19T11:09:36-08:00xapplehttp://code.activestate.com/recipes/users/4189256/http://code.activestate.com/recipes/578834-hierarchical-clustering-heatmap-python/

<p style="color: grey"> Python recipe 578834 by <a href="/recipes/users/4189256/">xapple</a> (<a href="/recipes/tags/clustering/">clustering</a>, <a href="/recipes/tags/heatmap/">heatmap</a>, <a href="/recipes/tags/hierarchical/">hierarchical</a>, <a href="/recipes/tags/microarray/">microarray</a>, <a href="/recipes/tags/python/">python</a>, <a href="/recipes/tags/rnaseq/">rnaseq</a>). Revision 2. </p> <p>A python class that performs hierarchical clustering and displays a heatmap using scipy and matplotlib. Improved to be require only as input a pandas DataFrame.</p>