pheatmap for Python
Project description
pheatmap
pheatmap
for Python.
You can create a heatmap with its annotation bars, just like pheatmap of R.
Requirements
pheatmap
need python
> 3.8, and numpy
, pandas
and matplolib
.
Install
You can install pheatmap
by pip
.
pip install pheatmap
Run the command above, pip
will automatically install numpy
, pandas
and matplolib
.
Usage
import numpy as np
import pandas as pd
from pheatmap import pheatmap
nrows, ncols = 10, 10
mat = np.linspace(-1, 1, nrows * ncols).reshape(nrows, ncols)
rownames = ["abcdefghig"[i % 10] for i in np.arange(nrows)]
colnames = ["xyz"[i % 3] for i in np.arange(ncols)]
mat = pd.DataFrame(mat, index=rownames, columns=colnames)
anno_row = pd.DataFrame(dict(
anno1=np.linspace(0, 10, nrows),
anno2=["CNS"[i % 3] for i in np.arange(nrows)]
))
anno_col = pd.DataFrame(dict(
anno3=np.linspace(0, 20, ncols),
anno4=["ABC"[i % 3] for i in np.arange(ncols)]
))
anno_row_cmaps = {"anno1": "Blues", "anno2": "Set1"}
anno_col_cmaps = {"anno3": "Purples", "anno4": "Set3"}
fig = pheatmap(
self.mat, annotation_row=self.anno_row, annotation_col=self.anno_col,
annotation_row_cmaps=self.anno_row_cmaps, annotation_col_cmaps=self.anno_col_cmaps
)
fig.savefig("tests/pheatmap.png")
Run the above code at the ipython or jupyter notebook. You can see the fellow heatmap with its annotation bars.
Also, you can save the figure to file. For example, save the figure to PDF
file.
fig.savefig("pheatmap.pdf")
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