# apafea
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* [Description](#description)
* [Installation](#installation)
* [Usage](#usage)
* [History](#history)
### Description
apafea is short for "alluvial plots as functional enrichment analysis".\
And it does just that. Input a set of gene clusters (supports KeyPathwayMiner & BiCoN) and apafea performs gene set enrichment analysis and shows an alluvial plot visualizing the results.\
For further Information check out [usage](#usage).
### Installation
Install the package with:
```pip install apafea```
#### Dependencies
* gseapy == 0.10.8
* plotly == 5.6.0
### Usage
###### python:
```python
from apafea import run
run(
mode="KPM",
data="/absolute/path/to/directory/",
mode_2="BiCoN",
data_2="/absolute/path/to/results.csv",
gsea_dir="/absolute/path/to/gsea/directory/",
GO=["bp",
"cc",
"mf",
"pw"],
PW=["KEGG",
"Reactome",
"WikiPathways",
"MSigDB_C",
"MSigDB_O_S"],
all=False,
cutoff=0.05,
)
```
###### explanation:
* "mode" - defines the type of input.
* "KPM" - give the path to your KeyPathwayMiner output directory under "data"
* "BiCoN" - give the path to your BiCoN result .csv file under "data"
* "custom" - give the path to your directory under "data" containing 1 cluster per file like this:
```
gene1
gene2
...
```
+ "mode_2" - defines the type of input for cluster comparison analysis.
* "KPM" - same as above
* "BiCoN" - same as above
* "custom" - same as above
* None / not set - cluster comparison analysis will not be performed
* "gsea_dir" - give the path to a directory to be used as gene set enrichment analysis output directory (default: /tmp)
* "GO" - list of GO-Terms enrichment analysis is being performed for
* "bp" - Biological process
* "cc" - Cellular Component
* "mf" - molecular Function
* "pw" - KEGG Pathways
* None / [] / not set - analysis will not be performed
* "PW" - list of pathway databases enrichment analysis is being performed for
* "KEGG" - KEGG_2016
* "Reactome" - Reactome_2016
* "WikiPathways" - WikiPathways_2016
* "MSigDB_C" - MSigDB_Computational
* "MSigDB_O_S" - MSigDB_Oncogenic_Signatures
* None / [] / not set - analysis will not be performed
* "all" - associates all its terms to a gene (default: False)
* "cutoff" - defines the cutoff for gene set enrichment analysis (default: 0.05)
### History
* 0.0.0 - initial commit
* 0.0.1 - first official release
* 0.0.2 - added MANIFEST.in and changed relative path handling for sample data
* 0.0.3 - fixed bug with relative path handling for sample data
* 0.0.4 - fixed bug with relative path handling for sample data
* 0.0.5 - fixed bug with relative path handling for sample data
* 0.0.6 - fixed bug with relative path handling for sample data
* 0.0.7 - added dependencies
* 0.0.8 - added adjustable font size feature
* 0.0.9 - added adjustable edge thicness feature
