Fold Change Violin Plot

Version: 1.0.0

Commit Hash: 5f8d5737d713e9646c60b9df504fd791dc4fc070

Author: CauldronGO Team

Category: visualization

Generate violin plots for fold enrichment analysis across organelles

Install with Cauldron get_app
README

Fold Change Violin Plot

Installation

⬇️ Click here to install in Cauldron (requires Cauldron to be running)

Repository: https://github.com/noatgnu/fold-change-violin-plugin

Manual installation:

  1. Open Cauldron
  2. Go to Plugins → Install from Repository
  3. Paste: https://github.com/noatgnu/fold-change-violin-plugin
  4. Click Install

ID: fold-change-violin
Version: 1.0.0
Category: visualization
Author: CauldronGO Team

Description

Generate violin plots for fold enrichment analysis across organelles

Runtime

  • Environments: python

  • Entrypoint: fold_change_violin_plot.py

Inputs

Name Label Type Required Default Visibility
input_file Input Data File file Yes - Always visible
columns_prefix Columns Prefix text No Difference Always visible
categories Organelle Columns column-selector (multiple) Yes - Always visible
match_value Match Value text No + Always visible
fold_enrichment_col Fold Enrichment Column text No Fold enrichment Always visible
organelle_col Organelle Column text No Organelle Always visible
comparison_col Comparison Column text No Comparison Always visible
colors Category Colors color-map (keys from categories) No - Always visible
figsize Figure Size text No 6,10 Always visible

Input Details

Input Data File (input_file)

Data file containing fold enrichment values

Columns Prefix (columns_prefix)

Prefix of columns to include in analysis

Organelle Columns (categories)

Select columns representing different organelles/categories

  • Column Source: input_file

Match Value (match_value)

Symbol or string to match in the data for filtering

Fold Enrichment Column (fold_enrichment_col)

Name of the column containing fold enrichment values

Organelle Column (organelle_col)

Name of the column containing organelle labels

Comparison Column (comparison_col)

Name of the column for comparison groups (optional)

Category Colors (colors)

Assign colors to each category/organelle

  • Input Type: Color map for assigning colors to categories
  • Keys From: categories (categories are derived from this input)

Figure Size (figsize)

Figure size in inches (width,height)

Outputs

Name File Type Format Description
violin_plots_pdf *.pdf image pdf Violin plots for each comparison group (PDF format)
violin_plots_svg *.svg image svg Violin plots for each comparison group (SVG format)

Visualizations

This plugin generates 1 plot(s):

Violin Plots (violin_plots)

  • Type: image-grid
  • Data Source: violin_plots_svg
  • Image Pattern: *.svg

Requirements

  • Python Version: >=3.11

Package Dependencies (Inline)

Packages are defined inline in the plugin configuration:

  • pandas>=2.0.0
  • seaborn>=0.12.0
  • matplotlib>=3.7.0

Note: When you create a custom environment for this plugin, these dependencies will be automatically installed.

Example Data

This plugin includes example data for testing:

  match_value: +
  fold_enrichment_col: Fold enrichment
  organelle_col: Organelle
  comparison_col: Comparison
  input_file: examples/fold_change/enrichment.txt
  categories_source: examples/fold_change/enrichment.txt
  categories: [C..Lysosome C..Mitochondria Endosome Golgi ER Ribosome Nuclear]
  columns_prefix: Difference

Load example data by clicking the Load Example button in the UI.

Usage

Via UI

  1. Navigate to visualization → Fold Change Violin Plot
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('fold-change-violin', {
  // Add parameters here
});