PopulaPy

Python (numpy/scipy/pandas/matplotlib) based Visualization tool for population structure data as generated with Illumina SNP chips.

plotPCA

Various versions to plot PCA (as calculated by plink --pca) together with ADMIXTURE information: every point is a piechart. plotPCA3 also contains a (repeated) subsampling procedure, as well as exclusion of populations that are less relevant.

Dependencies:

plink output files
pandas
matplotlib
python 3

The Python scripts are supposed to be used as examplary.

Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
4Genomes		4Genomes
Notebook		Notebook
README.md		README.md
assignPop.py		assignPop.py
fst.py		fst.py
fst_eval.py		fst_eval.py
makepop.py		makepop.py
pairwiseFst.py		pairwiseFst.py
pca100.png		pca100.png
ped2df.py		ped2df.py
plotPCA.py		plotPCA.py
plotPCA2.py		plotPCA2.py
plotPCA3.py		plotPCA3.py
scatterpie.py		scatterpie.py
selectPops.py		selectPops.py
selectPopsUAE.py		selectPopsUAE.py
visualizeDM.py		visualizeDM.py

HenschelLab/PopulaPy

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PopulaPy

plotPCA

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