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## Overview
This README file discusses the code associated with the manuscript:
Ke Yuan, Thomas Sakoparnig, Florian Markowetz and Niko Beerenwinkel. (2015)
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biology. Accepted
The Python code is based on the implementation from
Ryan Prescott Adams, Zoubin Ghahramani and Michael I. Jordan. (2010)
Tree-Structured Stick Breaking for Hierarchical Data. NIPS.
http://hips.seas.harvard.edu/files/tssb.tgz
---BitPhylogeny is licensed under the GPL v3, see the LICENSE.txt file for details.
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Python 2.7.6:
- NumPy 1.9.2,
- SciPy 0.15.1,
- scikit-learn 0.16.1: http://scikit-learn.org/stable/
- rpy2 2.5.6: http://rpy.sourceforge.net/
- pandas 0.16.1: http://pandas.pydata.org/
- h5py 2.5.0: http://www.h5py.org/
- python-igraph 0.7.1: http://igraph.org/python/
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R 3.2.0:
- rPython 0.0-6
- mcclust 1.0
- e1071 1.6-7
- igraph 0.7.1
- gplots 2.17.0
- riverplot 0.5
- plyr 1.8.2.
Clone the BitPhylogeny repository:
git clone git@bitbucket.org:ke_yuan/bitphylogeny.git
cd bitphylogeny
Install the BitPhylogeny python package:
cd python
sudo python setup.py install
Install the R package:
cd ../R
R CMD INSTALL bitphylogenyR_0.99.tar.gz
We've provided a sample data file 'sample_data.csv' in the python folder. To run the sample file, execute the following code.
BitPhylogeny analyse 'sample_data.csv' 'output' -true_label -n 200 -b 10 -t 5 -mode "methylation" -seed 1234
'sample_data.csv': the data file. Please make sure rows represent data points, colums represent dimension
'output': the output folder where the MCMC traces and tree scripts are stored.
-true_label: data file contains true labels as the last column.
-n: number of mcmc samples in total
-b: number of burn-in samples
-t: thin number (a current requirement is (number of mcmc samples / thin) > 5)
-mode: "methylation" or "mutation"
-seed: default 1234
-row_names: the first colum of the data file is row names
-collect_all_trees: option to store all trees (default: false)
The output folder contains the mcmc-traces, treescripts, alltreescripts (if -collect_all_trees is flagged).
For post processing, please use the accompanying R package. Tutorials of the R package are stored in doc/ directory For instruction on the Bitphylogeny graph, please find doc/bitphylogeny_node.html