Estimation Plot

Version: 1.0.0

Commit Hash: 7e57b6c96f647323e2c6b458fece05a2f9f10b7b

Author: CauldronGO Team

Category: visualization

Generate estimation plots with effect sizes using DABEST

Install with Cauldron get_app
README

Estimation Plot

ID: estimation-plot
Version: 1.0.0
Category: visualization
Author: CauldronGO Team

Description

Generate estimation plots with effect sizes using DABEST

Runtime

  • Type: python
  • Script: estimation_plot.py

Inputs

Name Label Type Required Default Visibility
input_file Input Data File file Yes - Always visible
annotation_file Sample Annotation File file Yes - Always visible
index_col Index Column text Yes - Always visible
selected_proteins Selected Proteins/Features text Yes - Always visible
log2 Apply Log2 Transformation boolean No true Always visible
condition_order Condition Order text No - Always visible

Input Details

Input Data File (input_file)

Data file containing protein/feature intensities

Sample Annotation File (annotation_file)

Sample annotation file with conditions

Index Column (index_col)

Column name to use as feature identifier (e.g., Protein.IDs)

Selected Proteins/Features (selected_proteins)

List of proteins/features to plot (one per line or comma-separated)

Apply Log2 Transformation (log2)

Apply log2 transformation to values before plotting

Condition Order (condition_order)

Comma-separated list of conditions in desired order

  • Placeholder: Control,Treatment1,Treatment2

Outputs

Name File Type Format Description
estimation_plots *.svg image svg Estimation plots for each selected protein (one SVG per protein)
statistics *_stats.tsv data tsv Statistical test results for each protein

Visualizations

This plugin generates 1 plot(s):

Estimation Plots (estimation_plots)

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

Requirements

  • Python: >=3.11
  • Packages:
  • pandas>=2.0.0
  • numpy>=1.24.0
  • dabest>=2023.2.14
  • matplotlib>=3.7.0

Example Data

This plugin includes example data for testing:

  index_col: Precursor.Id
  selected_proteins: AAAAAAPAGGPAAAAPSGENEAESR3,AAAAADLANR2,AAAAATVVPPMVGGPPFVGPVGFGPADR3
  log2: true
  input_file: diann/imputed.data.txt
  annotation_file: differential_analysis/annotation.txt

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

Usage

Via UI

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

Via Plugin System

const jobId = await pluginService.executePlugin('estimation-plot', {
  // Add parameters here
});