# pheatmap
[](https://codecov.io/gh/Ann-Holmes/pheatmap)
`pheatmap` for Python.
You can create a heatmap with its annotation bars, just like pheatmap of R. Documnets at [here](https://pheatmap.readthedocs.io/en/latest/)
## Requirements
`pheatmap` need `python` > 3.8, and `numpy`, `pandas` and `matplolib`.
## Install
You can install `pheatmap` by `pip`.
```shell
pip install pheatmap
```
Run the command above, `pip` will automatically install `numpy`, `pandas` and `matplolib`.
## Usage
```python
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.
```python
fig.savefig("pheatmap.pdf")
```
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