OmicEZ is a lightweight graphical tool designed for rapid visualization of differential expression and omics datasets. The software enables users to generate publication-quality heatmaps and volcano plots through an intuitive graphical interface without requiring programming knowledge.

The tool is particularly useful for researchers working with RNA-seq, methylation, proteomics, or other high-throughput omics datasets, where quick exploratory visualization and figure preparation are essential.

OmicEZ integrates customizable visualization options, hierarchical clustering, pathway highlighting, and flexible plotting parameters to streamline data interpretation.

Key Features

1. Heatmap Visualization

OmicEZ supports advanced heatmap generation with multiple customization options.

Clustering Options

• Hierarchical clustering of rows (genes) and/or columns (samples)

• Multiple clustering linkage methods:

  • Average

  • Single

  • Complete

  • Ward

  • Centroid

Visualization Controls

• Multiple color palettes for data representation

• Optional square cells for compact figure layout

• Automatic figure scaling based on number of genes and samples

• Adjustable clustering options for row and column dendrograms

• Non-overlapping color legends positioned outside the heatmap

Output

• Publication-ready heatmaps suitable for manuscripts and presentations

• High-resolution figure export

2. Volcano Plot Visualization

The volcano plot module provides a flexible framework for visualizing differential expression results.

Statistical Classification

Genes are automatically classified into four categories:

Each category is represented with a distinct color for clear interpretation.

Adjustable Thresholds

Users can define:

• Fold change cutoff

• P-value significance cutoff

These thresholds dynamically update the volcano plot.

Gene Highlighting

Specific genes can be highlighted by entering gene names.

Highlighted genes are visually emphasized for easier interpretation.

Pathway Highlighting

OmicEZ supports highlighting of genes belonging to specific biological pathways.

Features include:

• Multiple pathway selection

• Unique marker shapes for each pathway

• Non-overlapping pathway legends

• Automatic detection of genes belonging to selected pathways

Visual Customization

Additional customization options include:

• Dot shape selection

• Adjustable plot size

• External legends for improved readability

• Enhanced plot layout suitable for publication figures

Graphical User Interface (GUI)

OmicEZ provides a simple graphical interface built using PyQt, enabling users to perform visualization tasks without writing code.

The GUI contains two primary modules:

Heatmap Module

Options available:

• Load expression data file

• Select color palette

• Enable row clustering

• Enable column clustering

• Choose clustering method

• Enable square heatmap cells

• Plot heatmap

Volcano Module

Options available:

• Load differential expression file

• Define fold-change threshold

• Define p-value threshold

• Select dot shape

• Highlight specific genes

• Highlight biological pathways

• Generate volcano plot

Input Data Format

Heatmap Input

The heatmap module expects a gene expression matrix where rows represent genes and columns represent samples.

Example format:

Requirements:

• First column must contain gene names

• Remaining columns must contain numeric expression values

Supported formats:

• CSV

• TSV

Volcano Plot Input

The volcano module expects a differential analysis table with at least three columns.

Example format:

Required columns: