# gnr
<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
This file will become your README and also the index of your
documentation.
## Developer Guide
### Setup
``` sh
# create conda environment
$ mamba env create -f env.yml
# update conda environment
$ mamba env update -n gnr --file env.yml
# $ mamba env update -n gnr --file env.mac.yml
```
### Install
``` sh
pip install -e .
# install from pypi
pip install gnr
```
### nbdev
``` sh
# activate conda environment
$ conda activate gnr
# make sure the gnr package is installed in development mode
$ pip install -e .
# make changes under nbs/ directory
# ...
# compile to have changes apply to the gnr package
$ nbdev_prepare
```
Note: it might be useful to use the following snippet to enable hot
reloading:
``` python
%load_ext autoreload
%autoreload 2
```
### Publishing
``` sh
# publish to pypi
$ nbdev_pypi
# publish to conda
$ nbdev_conda --build_args '-c conda-forge'
```
# Usage
## Installation
Install latest from the GitHub
[repository](https://github.com/dsm-72/gnr):
``` sh
$ pip install git+https://github.com/dsm-72/gnr.git
```
or from [conda](https://anaconda.org/dsm-72/gnr)
``` sh
$ conda install -c dsm-72 gnr
```
or from [pypi](https://pypi.org/project/gnr/)
``` sh
$ pip install gnr
```
``` python
df_trj = make_mock_genes_x_tbins()
df_trj.head()
```
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
| | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ... | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 |
|-------|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
| wasf | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |
| colq | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | ... | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| gpr1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |
| chrm3 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | ... | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| lmod2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | ... | 8 | 8 | 8 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |
<p>5 rows × 100 columns</p>
</div>
``` python
gc_op = GrangerCausality(n_jobs=2)
```
``` python
df_res = gc_op.fit_transform(df_trj, fit_params={'standard_scaler':True, 'signed_correlation': True})
```
``` python
df_res.head()
```
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
| | wasf_y | colq_y | gpr1_y | chrm3_y | lmod2_y | tek_y | kank3_y | oca2_y | taz_y | map4k1_y |
|---------|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|
| wasf_x | 1.000000 | 0.683091 | 0.314458 | 0.144127 | 0.000818 | 1.000000 | 1.000000 | 0.000066 | 0.102470 | 0.006449 |
| colq_x | 1.000000 | 1.000000 | 0.779284 | 1.000000 | 1.000000 | 0.001091 | 0.192685 | 0.675090 | 1.000000 | 0.806543 |
| gpr1_x | 0.805541 | 0.042286 | 1.000000 | 0.892251 | 0.795418 | 0.823063 | 1.000000 | 0.542452 | 0.001091 | 0.852052 |
| chrm3_x | 0.001091 | 0.073638 | 0.168425 | 1.000000 | 0.632585 | 1.000000 | 0.102470 | 0.542452 | 1.000000 | 0.367649 |
| lmod2_x | 0.683091 | 0.000104 | 0.031086 | 0.220671 | 1.000000 | 0.683091 | 0.000818 | 0.367649 | 1.000000 | 0.017608 |
</div>
``` python
gc_op.plot_df_org(figsize=(4,4))
```
``` python
gc_op.plot_df_res(figsize=(4,4))
```
## Documentation
Documentation can be found hosted on GitHub
[repository](https://github.com/dsm-72/gnr)
[pages](https://dsm-72.github.io/gnr/). Additionally you can find
package manager specific guidelines on
[conda](https://anaconda.org/dsm-72/gnr) and
[pypi](https://pypi.org/project/gnr/) respectively.
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"description": "# gnr\n\n<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->\n\nThis file will become your README and also the index of your\ndocumentation.\n\n## Developer Guide\n\n### Setup\n\n``` sh\n# create conda environment\n$ mamba env create -f env.yml\n\n# update conda environment\n$ mamba env update -n gnr --file env.yml\n# $ mamba env update -n gnr --file env.mac.yml\n```\n\n### Install\n\n``` sh\npip install -e .\n\n# install from pypi\npip install gnr\n```\n\n### nbdev\n\n``` sh\n# activate conda environment\n$ conda activate gnr\n\n# make sure the gnr package is installed in development mode\n$ pip install -e .\n\n# make changes under nbs/ directory\n# ...\n\n# compile to have changes apply to the gnr package\n$ nbdev_prepare\n```\n\nNote: it might be useful to use the following snippet to enable hot\nreloading:\n\n``` python\n%load_ext autoreload\n%autoreload 2\n```\n\n### Publishing\n\n``` sh\n# publish to pypi\n$ nbdev_pypi\n\n# publish to conda\n$ nbdev_conda --build_args '-c conda-forge'\n```\n\n# Usage\n\n## Installation\n\nInstall latest from the GitHub\n[repository](https://github.com/dsm-72/gnr):\n\n``` sh\n$ pip install git+https://github.com/dsm-72/gnr.git\n```\n\nor from [conda](https://anaconda.org/dsm-72/gnr)\n\n``` sh\n$ conda install -c dsm-72 gnr\n```\n\nor from [pypi](https://pypi.org/project/gnr/)\n\n``` sh\n$ pip install gnr\n```\n\n``` python\ndf_trj = make_mock_genes_x_tbins()\ndf_trj.head()\n```\n\n<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n .dataframe tbody tr th {\n vertical-align: top;\n }\n .dataframe thead th {\n text-align: right;\n }\n</style>\n\n| | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ... | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 |\n|-------|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|\n| wasf | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |\n| colq | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | ... | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n| gpr1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |\n| chrm3 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | 9 | ... | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |\n| lmod2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | ... | 8 | 8 | 8 | 9 | 9 | 9 | 9 | 9 | 9 | 9 |\n\n<p>5 rows \u00d7 100 columns</p>\n</div>\n\n``` python\ngc_op = GrangerCausality(n_jobs=2)\n```\n\n``` python\ndf_res = gc_op.fit_transform(df_trj, fit_params={'standard_scaler':True, 'signed_correlation': True})\n```\n\n``` python\ndf_res.head()\n```\n\n<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n .dataframe tbody tr th {\n vertical-align: top;\n }\n .dataframe thead th {\n text-align: right;\n }\n</style>\n\n| | wasf_y | colq_y | gpr1_y | chrm3_y | lmod2_y | tek_y | kank3_y | oca2_y | taz_y | map4k1_y |\n|---------|----------|----------|----------|----------|----------|----------|----------|----------|----------|----------|\n| wasf_x | 1.000000 | 0.683091 | 0.314458 | 0.144127 | 0.000818 | 1.000000 | 1.000000 | 0.000066 | 0.102470 | 0.006449 |\n| colq_x | 1.000000 | 1.000000 | 0.779284 | 1.000000 | 1.000000 | 0.001091 | 0.192685 | 0.675090 | 1.000000 | 0.806543 |\n| gpr1_x | 0.805541 | 0.042286 | 1.000000 | 0.892251 | 0.795418 | 0.823063 | 1.000000 | 0.542452 | 0.001091 | 0.852052 |\n| chrm3_x | 0.001091 | 0.073638 | 0.168425 | 1.000000 | 0.632585 | 1.000000 | 0.102470 | 0.542452 | 1.000000 | 0.367649 |\n| lmod2_x | 0.683091 | 0.000104 | 0.031086 | 0.220671 | 1.000000 | 0.683091 | 0.000818 | 0.367649 | 1.000000 | 0.017608 |\n\n</div>\n\n``` python\ngc_op.plot_df_org(figsize=(4,4))\n```\n\n\n\n``` python\ngc_op.plot_df_res(figsize=(4,4))\n```\n\n\n\n## Documentation\n\nDocumentation can be found hosted on GitHub\n[repository](https://github.com/dsm-72/gnr)\n[pages](https://dsm-72.github.io/gnr/). Additionally you can find\npackage manager specific guidelines on\n[conda](https://anaconda.org/dsm-72/gnr) and\n[pypi](https://pypi.org/project/gnr/) respectively.\n",
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