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Matthias Ley committed Jan 20, 2023
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76 changes: 76 additions & 0 deletions .github/workflows/codeql.yml
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# For most projects, this workflow file will not need changing; you simply need
# to commit it to your repository.
#
# You may wish to alter this file to override the set of languages analyzed,
# or to provide custom queries or build logic.
#
# ******** NOTE ********
# We have attempted to detect the languages in your repository. Please check
# the `language` matrix defined below to confirm you have the correct set of
# supported CodeQL languages.
#
name: "CodeQL"

on:
push:
branches: [ "master" ]
pull_request:
# The branches below must be a subset of the branches above
branches: [ "master" ]
schedule:
- cron: '20 20 * * 2'

jobs:
analyze:
name: Analyze
runs-on: ubuntu-latest
permissions:
actions: read
contents: read
security-events: write

strategy:
fail-fast: false
matrix:
language: [ 'python' ]
# CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
# Use only 'java' to analyze code written in Java, Kotlin or both
# Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
# Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support

steps:
- name: Checkout repository
uses: actions/checkout@v3

# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v2
with:
languages: ${{ matrix.language }}
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.

# Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
# queries: security-extended,security-and-quality


# Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java).
# If this step fails, then you should remove it and run the build manually (see below)
- name: Autobuild
uses: github/codeql-action/autobuild@v2

# ℹ️ Command-line programs to run using the OS shell.
# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun

# If the Autobuild fails above, remove it and uncomment the following three lines.
# modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.

# - run: |
# echo "Run, Build Application using script"
# ./location_of_script_within_repo/buildscript.sh

- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v2
with:
category: "/language:${{matrix.language}}"
15 changes: 8 additions & 7 deletions README.md
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[![Build Status](https://app.travis-ci.com/Mnikley/OntoViz.svg?branch=master)](https://app.travis-ci.com/Mnikley/OntoViz)
[![image](https://img.shields.io/pypi/v/ontoviz-bio.svg)](https://pypi.python.org/pypi/ontoviz-bio)

OntoViz
=======
OntoloViz
=========

OntoViz is a graphical user interface for the creation of interactive visualizations of phenotype and drug ontologies.
OntoloViz is a graphical user interface for the creation of interactive sunburst plots of phenotype and drug ontologies.
You might find it useful to quickly visualize your data for reports or to share the generated plots with collaborators.
Take a look at the [screenshot section](#screenshots) or explore examples in `.html` format from the
provided [templates.zip](https://github.com/Mnikley/OntoViz/releases/download/v1.0.3/templates.zip) archive to get a
Expand Down Expand Up @@ -34,6 +34,8 @@ to integers.

GUI Options
-----------
![gui_small](https://user-images.githubusercontent.com/75040444/213717385-adb372a9-d0a4-4861-af9e-3fcb7a3c195d.jpg)

- General
- **Load File**: load an `.tsv` or `.xlsx` file containing drug- or phenotype-ontology data
- **Set Color Scale**: define a custom color scale for the sunburst color scaling when color propagation is active
Expand Down Expand Up @@ -62,7 +64,7 @@ GUI Options
- `level`: counts are propagated up to defined level, values above threshold remain unchanged
- `all`: counts are propagated up to central node, imported values are corrected and overwritten
- **Level**: controls color- and count-propagation from outer to inner levels up to defined level
- affects color propagation when **Color** is set to `specific` or `global`, affects
- affects color propagation when **Color** is set to `specific` or `global`
- affects count propagation when **Counts** is set to `level`
- drug sunburst: 1 corresponds to the central node, 5 to the outermost node (=drug)
- phenotype sunburst: 0 corresponds to the central node, 13 to the outermost node
Expand All @@ -73,7 +75,7 @@ The phenotype sunburst structure follows the principles of the
[MeSH tree](https://www.nlm.nih.gov/mesh/intro_trees.html).
- A Tree ID is defined by a **combination of three numbers or letters**, for example `C01`.
- Levels are separated by a **dot `.`**, for example `C01.001`.
- Ontologies **up to thirteen hierarchical levels** were tested, more should be possible though.
- Ontologies **up to thirteen hierarchical levels** are supported.
- A single phenotype end-node can be assigned to multiple parent-nodes by specifying the parents tree ids as
pipe separated string in the column `Tree ID`.
- When defining a child element which has no valid parent, the GUI will automatically generate the parent with the
Expand Down Expand Up @@ -127,7 +129,6 @@ Drug Ontology File Structure

Screenshots
===========
![gui](https://user-images.githubusercontent.com/75040444/213483108-0381b4c5-baf4-4489-8f98-b38562dd96d5.jpg)
![atc_sample](https://user-images.githubusercontent.com/75040444/213471039-78082a44-1be2-4864-9fd2-540c8f7f23bf.jpg)
![mesh_sample](https://user-images.githubusercontent.com/75040444/213471097-5257d612-510a-4f15-b65c-2fba8bf812ea.jpg)

Expand Down

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