# plot_him_matrix

**Reliability status**: `stable`

```{eval-rst}
.. argparse::
   :ref: traceratops.plot_him_matrix.parse_arguments
   :prog: plot_him_matrix
```


## Example

Here is examples usage of plot_him_matrix:

### Proximity matrix with all data (including bin with NaN value)
```bash
plot_him_matrix -M PWDscMatrix.npy -B unique_barcodes.ecsv --keep_nan
```

<p align="center">
    <img src="../../_static/Fig_PWDscMatrix_proximity_0.01-0.10.png" width="45%">
    <img src="../../_static/Fig_PWDscMatrix_proximity_norm_0.82-0.95_nan.png" width="45%">
</p>


### Default normalized VS. KDE (c_map: Spectral)


```bash
plot_him_matrix -M PWDscMatrix.npy -B unique_barcodes.ecsv
```

**VS.**

```bash
plot_him_matrix -M PWDscMatrix.npy -B unique_barcodes.ecsv --mode KDE --c_map Spectral
```

<p align="center">
    <img src="../../_static/Fig_PWDscMatrix_proximity_norm_0.20-0.59.png" width="45%">
    <img src="../../_static/Fig_PWDscMatrix_KDE_0.21-0.37.png" width="45%">
</p>