Geneview is a Python visualization library base on matplotlib. It provides a high-level interface for drawing attractive genomics graphics. And now it is actively developed.
We use a dataset
GOYA_previewwhich is in geneview-data repository, as the input for the plots below. Here is the format preview ofGOYA_preview:
A basic example for Manhattan plot.
import matplotlib.pyplot as plt
import geneview as gv
df = gv.util.load_dataset('GOYA_preview') # df is DataFrame of pandas
xtick = ['chr'+c for c in map(str, range(1, 15) + ['16', '18', '20', '22'])]
gv.gwas.manhattanplot(df[['chrID','position','pvalue']],
xlabel="Chromosome",
ylabel="-Log10(P-value)",
xticklabel_kws={'rotation': 'vertical'},
xtick_label_set = set(xtick))
plt.show()
A basic example for QQ plot.
import matplotlib.pyplot as plt
import geneview as gv
df = gv.util.load_dataset('GOYA_preview') # df is DataFrame of pandas
gv.gwas.qqplot(df['pvalue'], color="#00bb33",
xlabel="Expected p-value(-log10)",
ylabel="Observed p-value(-log10)")
plt.show()
- Python 2.7 or Python 3.4+
We need the data structures: DataFrame and Series in pandas. It's easy
and worth to learn, click here
to see more detail tutorial for these two data type.
To install the released version, just do
pip install geneview
You may instead want to use the development version from Github, by running
pip install git+git://github.com/ShujiaHuang/geneview.git#egg=geneview
Released under a BSD (3-clause) license