Bubble Plot Heat Map

Version: 1.0.0

Commit Hash: 5a566d319a6577cddd7bca5dba5de0da9784b6a7

Author: CauldronGO Team (based on noatgnu/bubble-plot)

Category: visualization

Create interactive bubble plot heat maps where bubble size and color represent intensity values across features and samples

Install with Cauldron get_app
README

Bubble Plot Heat Map

Installation

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

Repository: https://github.com/noatgnu/bubble-plot-plugin

Manual installation:

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

ID: bubble-plot
Version: 1.0.0
Category: visualization
Author: CauldronGO Team (based on noatgnu/bubble-plot)

Description

Create interactive bubble plot heat maps where bubble size and color represent intensity values across features and samples

Runtime

  • Environments: python

  • Entrypoint: bubble_plot.py

Inputs

Name Label Type Required Default Visibility
input_file Input Data File file Yes - Always visible
separator Column Separator select ( , ,, ;) No Always visible
log_transform Apply Log10 Transformation boolean No true Always visible
colormap Color Scheme select (yellow_red, blue_red, green_purple, viridis, plasma) No yellow_red Always visible
min_radius Minimum Bubble Size number (min: 0, max: 0, step: 0) No 0.2 Always visible
max_radius Maximum Bubble Size number (min: 0, max: 1, step: 0) No 0.5 Always visible
output_format Output Format select (png, pdf, both) No both Always visible
dpi Resolution (DPI) number (min: 72, max: 600, step: 50) No 300 Always visible

Input Details

Input Data File (input_file)

Wide-format data table with features in first column and samples in subsequent columns (e.g., peptide_intensities_wide.txt from MSstatsPTM)

Column Separator (separator)

Character used to separate columns in the input file

  • Options: , ,, ;

Apply Log10 Transformation (log_transform)

Apply log10 transformation to intensity values for better visualization of dynamic range

Color Scheme (colormap)

Color palette for representing intensity values

  • Options: yellow_red, blue_red, green_purple, viridis, plasma

Minimum Bubble Size (min_radius)

Minimum radius for bubbles representing lowest values

Maximum Bubble Size (max_radius)

Maximum radius for bubbles representing highest values

Output Format (output_format)

File format(s) for output visualization

  • Options: png, pdf, both

Resolution (DPI) (dpi)

Output resolution in dots per inch (higher values = better quality but larger file size)

Outputs

Name File Type Format Description
bubble_plot_png bubble_plot.png plot png Bubble plot heat map visualization in PNG format
bubble_plot_pdf bubble_plot.pdf plot pdf Bubble plot heat map visualization in PDF format

Requirements

  • Python Version: >=3.8

Python Dependencies (External File)

Dependencies are defined in: requirements.txt

  • pandas>=2.0.0
  • numpy>=1.24.0
  • matplotlib>=3.7.0

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

Usage

Via UI

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

Via Plugin System

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