# Jeddinformatics
## Initial setup
```bash
pip install -r requirements.txt
```
This will install the required packages
## Running on errything
```bash
python3 main.py <your data folder>
```
## TODO
- [ ] make sure non cancer is always first
- [ ] change boxes and whiskers to be a different colour
- [ ] remove shading
## Config files
```json
{
"$schema": "https://raw.githubusercontent.com/wolffshots/jeddinformatics/main/src/jeddinformatics/schema.json",
"mappings": {
"normal": "NC",
"Normal": "NC",
"OV": "OV",
"UCEC": "UCEC",
"Ovarian Cancer": "OV",
"Uterine Cancer": "UCEC",
"Some title": "Translated title",
"log2(TPM)": "log₂(TPM)"
},
"colors": {
"NC": "blue",
"OV": "green",
"UCEC": "red",
"box": "black",
"plot_background_color": "lightgray",
"paper_background_color": "white"
},
"precedence": ["NC", "normal", "Normal"],
"jitter": 0.5,
"line_width": 1.5,
"point_size": 6,
"plot_height": 540,
"plot_width": 960
}
```
## Building and distributing
```bash
rm -fr dist && python3 -m build && python3 -m twine upload --repository testpypi dist/*
```
Rename all to OV (Ovarian canver) and UCEC (Uterine cancer) and make "normal"/"Normal" to NC (Non-cancer)
Data should look like:
```
│
├───Gene Expression
│ └───ONCODB
│ ├───Ovarian Cancer
│ │ ├───CAS
│ │ │ data.txt
│ │ │
│ │ ├───IPO5
│ │ │ data.txt
│ │ │
│ │ ├───KPNA2
│ │ │ data.txt
│ │ │
│ │ ├───KPNB1
│ │ │ data.txt
│ │ │
│ │ ├───RAN
│ │ │ data.txt
│ │ │
│ │ ├───TNPO1
│ │ │ data.txt
│ │ │
│ │ └───XPO1
│ │ data.txt
│ │
│ └───Uterine Cancer
│ ├───CAS
│ │ data.txt
│ │
│ ├───IPO5
│ │ data.txt
│ │
│ ├───KPNA2
│ │ data.txt
│ │
│ ├───KPNB1
│ │ data.txt
│ │
│ ├───RAN
│ │ data.txt
│ │
│ ├───TNPO1
│ │ data.txt
│ │
│ └───XPO1
│ data.txt
│
└───Protein Expression
└───UALCAN
├───Ovarian Cancer
│ ├───CAS
│ │ data.json
│ │
│ ├───IPO5
│ │ data.json
│ │
│ ├───KPNA2
│ │ data.json
│ │
│ ├───KPNB1
│ │ data.json
│ │
│ ├───RAN
│ │ data.json
│ │
│ ├───TNPO1
│ │ data.json
│ │
│ └───XPO1
│ data.json
│
└───Uterine Cancer
├───CAS
│ data.json
│
├───IPO5
│ data.json
│
├───KPNA2
│ data.json
│
├───KPNB1
│ data.json
│
├───RAN
│ data.json
│
├───TNPO1
│ data.json
│
└───XPO1
data.json
```
So general form is:
```
{gene or protein expression}
└───{source database}
└───{type of cancer}
└───{gene or protein name}
└───{data.json or data.txt}
```
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"description": "# Jeddinformatics\n\n## Initial setup\n```bash\npip install -r requirements.txt\n```\nThis will install the required packages\n\n## Running on errything\n```bash\npython3 main.py <your data folder>\n```\n\n## TODO\n- [ ] make sure non cancer is always first\n- [ ] change boxes and whiskers to be a different colour\n- [ ] remove shading\n\n## Config files\n```json\n{\n \"$schema\": \"https://raw.githubusercontent.com/wolffshots/jeddinformatics/main/src/jeddinformatics/schema.json\",\n \"mappings\": {\n \"normal\": \"NC\",\n \"Normal\": \"NC\",\n \"OV\": \"OV\",\n \"UCEC\": \"UCEC\",\n \"Ovarian Cancer\": \"OV\",\n \"Uterine Cancer\": \"UCEC\",\n \"Some title\": \"Translated title\",\n \"log2(TPM)\": \"log\u2082(TPM)\"\n },\n \"colors\": {\n \"NC\": \"blue\",\n \"OV\": \"green\",\n \"UCEC\": \"red\",\n \"box\": \"black\",\n \"plot_background_color\": \"lightgray\",\n \"paper_background_color\": \"white\"\n },\n \"precedence\": [\"NC\", \"normal\", \"Normal\"],\n \"jitter\": 0.5,\n \"line_width\": 1.5,\n \"point_size\": 6,\n \"plot_height\": 540,\n \"plot_width\": 960\n}\n```\n\n## Building and distributing\n```bash\nrm -fr dist && python3 -m build && python3 -m twine upload --repository testpypi dist/*\n```\n\nRename all to OV (Ovarian canver) and UCEC (Uterine cancer) and make \"normal\"/\"Normal\" to NC (Non-cancer)\n\nData should look like:\n```\n\u2502 \n\u251c\u2500\u2500\u2500Gene Expression\n\u2502 \u2514\u2500\u2500\u2500ONCODB\n\u2502 \u251c\u2500\u2500\u2500Ovarian Cancer\n\u2502 \u2502 \u251c\u2500\u2500\u2500CAS\n\u2502 \u2502 \u2502 data.txt\n\u2502 \u2502 \u2502 \n\u2502 \u2502 \u251c\u2500\u2500\u2500IPO5\n\u2502 \u2502 \u2502 data.txt\n\u2502 \u2502 \u2502 \n\u2502 \u2502 \u251c\u2500\u2500\u2500KPNA2\n\u2502 \u2502 \u2502 data.txt\n\u2502 \u2502 \u2502 \n\u2502 \u2502 \u251c\u2500\u2500\u2500KPNB1\n\u2502 \u2502 \u2502 data.txt\n\u2502 \u2502 \u2502 \n\u2502 \u2502 \u251c\u2500\u2500\u2500RAN\n\u2502 \u2502 \u2502 data.txt\n\u2502 \u2502 \u2502 \n\u2502 \u2502 \u251c\u2500\u2500\u2500TNPO1\n\u2502 \u2502 \u2502 data.txt\n\u2502 \u2502 \u2502 \n\u2502 \u2502 \u2514\u2500\u2500\u2500XPO1\n\u2502 \u2502 data.txt\n\u2502 \u2502 \n\u2502 \u2514\u2500\u2500\u2500Uterine Cancer\n\u2502 \u251c\u2500\u2500\u2500CAS\n\u2502 \u2502 data.txt\n\u2502 \u2502 \n\u2502 \u251c\u2500\u2500\u2500IPO5\n\u2502 \u2502 data.txt\n\u2502 \u2502 \n\u2502 \u251c\u2500\u2500\u2500KPNA2\n\u2502 \u2502 data.txt\n\u2502 \u2502 \n\u2502 \u251c\u2500\u2500\u2500KPNB1\n\u2502 \u2502 data.txt\n\u2502 \u2502 \n\u2502 \u251c\u2500\u2500\u2500RAN\n\u2502 \u2502 data.txt\n\u2502 \u2502 \n\u2502 \u251c\u2500\u2500\u2500TNPO1\n\u2502 \u2502 data.txt\n\u2502 \u2502 \n\u2502 \u2514\u2500\u2500\u2500XPO1\n\u2502 data.txt\n\u2502 \n\u2514\u2500\u2500\u2500Protein Expression\n \u2514\u2500\u2500\u2500UALCAN\n \u251c\u2500\u2500\u2500Ovarian Cancer\n \u2502 \u251c\u2500\u2500\u2500CAS\n \u2502 \u2502 data.json\n \u2502 \u2502 \n \u2502 \u251c\u2500\u2500\u2500IPO5\n \u2502 \u2502 data.json\n \u2502 \u2502 \n \u2502 \u251c\u2500\u2500\u2500KPNA2\n \u2502 \u2502 data.json\n \u2502 \u2502 \n \u2502 \u251c\u2500\u2500\u2500KPNB1\n \u2502 \u2502 data.json\n \u2502 \u2502 \n \u2502 \u251c\u2500\u2500\u2500RAN\n \u2502 \u2502 data.json\n \u2502 \u2502 \n \u2502 \u251c\u2500\u2500\u2500TNPO1\n \u2502 \u2502 data.json\n \u2502 \u2502 \n \u2502 \u2514\u2500\u2500\u2500XPO1\n \u2502 data.json\n \u2502 \n \u2514\u2500\u2500\u2500Uterine Cancer\n \u251c\u2500\u2500\u2500CAS\n \u2502 data.json\n \u2502 \n \u251c\u2500\u2500\u2500IPO5\n \u2502 data.json\n \u2502 \n \u251c\u2500\u2500\u2500KPNA2\n \u2502 data.json\n \u2502 \n \u251c\u2500\u2500\u2500KPNB1\n \u2502 data.json\n \u2502 \n \u251c\u2500\u2500\u2500RAN\n \u2502 data.json\n \u2502 \n \u251c\u2500\u2500\u2500TNPO1\n \u2502 data.json\n \u2502 \n \u2514\u2500\u2500\u2500XPO1\n data.json\n \n```\n\nSo general form is:\n```\n {gene or protein expression}\n \u2514\u2500\u2500\u2500{source database}\n \u2514\u2500\u2500\u2500{type of cancer}\n \u2514\u2500\u2500\u2500{gene or protein name}\n \u2514\u2500\u2500\u2500{data.json or data.txt}\n```\n",
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