apafea 0.0.9

Description:

apafea 0.0.9

apafea
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Description
Installation
Usage
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.
Installation
Install the package with:
pip install apafea
Dependencies

gseapy == 0.10.8
plotly == 5.6.0

Usage
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