Correlation Matrix

Version: 1.0.0

Commit Hash: 9ca33eda3fa98e53405291b5fbb01c8ccd44afcf

Author: CauldronGO Team

Category: visualization

Generate correlation matrices with customizable visualization options

Install with Cauldron get_app
README

Correlation Matrix

Installation

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

Repository: https://github.com/noatgnu/correlation-matrix-plugin

Manual installation:

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

ID: correlation-matrix
Version: 1.0.0
Category: visualization
Author: CauldronGO Team

Description

Generate correlation matrices with customizable visualization options

Runtime

  • Environments: r

  • Entrypoint: correlation_matrix.R

Inputs

Name Label Type Required Default Visibility
input_file Input File file Yes - Always visible
index_col Index Column text No - Always visible
sample_cols Sample Columns column-selector (multiple) Yes - Always visible
method Correlation Method select (pearson, spearman, kendall) No pearson Always visible
min_value Minimum Value number No 0 Always visible
order Order select (original, AOE, FPC, hclust, alphabet) No - Always visible
hclust_method Hierarchical Clustering Method select (ward.D, ward.D2, single, complete, average, mcquitty, median, centroid) No ward.D Always visible
presenting_method Presentation Method select (circle, square, ellipse, number, shade, color, pie) No ellipse Always visible
cor_shape Correlation Shape select (full, upper, lower) No upper Always visible
plot_only Plot Only (Skip Correlation) boolean No false Always visible
color_ramp_palette Color Palette text No - Always visible
plot_width Plot Width number (min: 5, max: 30) No 10 Always visible
plot_height Plot Height number (min: 5, max: 30) No 10 Always visible
text_label_size Text Label Size number (min: 0, max: 5, step: 0) No 1 Always visible
number_label_size Number Label Size number (min: 0, max: 5, step: 0) No 1 Always visible
label_rotation Label Rotation number (min: 0, max: 90, step: 5) No 45 Always visible
show_diagonal Show Diagonal boolean No true Always visible
add_grid Add Grid boolean No false Always visible
grid_color Grid Color color (color picker) No #000000 Always visible
number_digits Number of Digits number (min: 0, max: 5, step: 1) No 2 Always visible
plot_title Plot Title text No - Always visible
use_basename Use Basename Only boolean No true Always visible
max_label_length Max Label Length number (min: 10, max: 200, step: 5) No 50 Always visible

Input Details

Input File (input_file)

Data file for correlation analysis

Index Column (index_col)

Column name to use as row identifier

Sample Columns (sample_cols)

Columns to include in correlation analysis

  • Column Source: input_file

Correlation Method (method)

Method for calculating correlations

  • Options: pearson, spearman, kendall

Minimum Value (min_value)

Minimum value for filtering

Order (order)

Ordering method for variables

  • Options: original, AOE, FPC, hclust, alphabet

Hierarchical Clustering Method (hclust_method)

Method for hierarchical clustering

  • Options: ward.D, ward.D2, single, complete, average, mcquitty, median, centroid

Presentation Method (presenting_method)

Visual representation of correlations

  • Options: circle, square, ellipse, number, shade, color, pie

Correlation Shape (cor_shape)

Which part of the matrix to display

  • Options: full, upper, lower

Plot Only (Skip Correlation) (plot_only)

Plot the input data directly without computing correlations

Color Palette (color_ramp_palette)

Color palette for the plot

  • Placeholder: RdYlBu,Blues,Greens

Plot Width (plot_width)

Width of the plot in inches

Plot Height (plot_height)

Height of the plot in inches

Text Label Size (text_label_size)

Size of text labels

Number Label Size (number_label_size)

Size of correlation coefficient numbers

Label Rotation (label_rotation)

Rotation angle for labels in degrees

Show Diagonal (show_diagonal)

Show the diagonal of the correlation matrix

Add Grid (add_grid)

Add grid lines to the plot

Grid Color (grid_color)

Color of grid lines (if enabled)

  • Input Type: Color picker for selecting a single color value

Number of Digits (number_digits)

Decimal places for correlation coefficients

Plot Title (plot_title)

Title for the correlation plot

Use Basename Only (use_basename)

Extract only the filename from full file paths

Max Label Length (max_label_length)

Maximum length for axis labels (characters)

Outputs

Name File Type Format Description
correlation_matrix correlation_matrix.txt data tsv Correlation matrix values
correlation_plot_pdf correlation_matrix.pdf image pdf Correlation matrix visualization (PDF)
correlation_plot_svg correlation_matrix.svg image svg Correlation matrix visualization (SVG)

Visualizations

This plugin generates 1 plot(s):

Correlation Matrix (correlation_plot)

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

Requirements

  • R Version: >=4.0

Package Dependencies (Inline)

Packages are defined inline in the plugin configuration:

  • corrplot
  • RColorBrewer

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:

  presenting_method: ellipse
  color_ramp_palette: #053061,#2166AC,#4393C3,#92C5DE,#D1E5F0,#FFFFFF,#FDDBC7,#F4A582,#D6604D,#B2182B,#67001F
  max_label_length: 50
  index_col: Precursor.Id
  method: pearson
  order: hclust
  cor_shape: upper
  use_basename: true
  input_file: diann/imputed.data.txt
  sample_cols_source: diann/imputed.data.txt
  sample_cols: [C:\Raja\DIA-NN searches\June 2022\LT-CBQCA-Test_DIA\RN-DS_220106_BCA_LT-IP_01.raw C:\Raja\DIA-NN searches\June 2022\LT-CBQCA-Test_DIA\RN-DS_220106_BCA_LT-IP_02.raw C:\Raja\DIA-NN searches\June 2022\LT-CBQCA-Test_DIA\RN-DS_220106_BCA_LT-IP_03.raw C:\Raja\DIA-NN searches\June 2022\LT-CBQCA-Test_DIA\RN-DS_220106_BCA_LT-MockIP_01.raw C:\Raja\DIA-NN searches\June 2022\LT-CBQCA-Test_DIA\RN-DS_220106_BCA_LT-MockIP_02.raw C:\Raja\DIA-NN searches\June 2022\LT-CBQCA-Test_DIA\RN-DS_220106_BCA_LT-MockIP_03.raw]
  hclust_method: ward.D

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

Usage

Via UI

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

Via Plugin System

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