Documentation/Analysis/Data Visualization

Data Visualization

Advanced visualization tools for molecular structures, data analysis, and scientific plotting with interactive 3D viewers and publication-ready outputs.

Molecular Visualization Nodes

Specialized nodes for visualizing molecular structures and interactions.

2D Structure Drawing

Draw 2D molecular structures from RDKit molecules or SMILES strings

Type: structure_draw_2dCategory: Molecular Visualization

Key Features

  • •Multiple rendering modes (single, grid, auto)
  • •Customizable cell dimensions
  • •Atom index annotations
  • •Background color control
  • •High-resolution output

Input Ports

moleculesmolecules

RDKit molecules to visualize

smiles_dfdata

DataFrame with SMILES strings

smilesstring

Single SMILES string

Output Ports

imageimage

PNG image of structures

bytesbytes

Raw PNG bytes

3D Molecular Viewer

Interactive 3D molecular viewer using NGL.js web technology

Type: web3d_viewerCategory: Molecular Visualization

Key Features

  • •Interactive 3D rotation and zoom
  • •Multiple rendering styles (ball-and-stick, cartoon, surface)
  • •Distance and angle measurements
  • •Animation support
  • •Export capabilities

Input Ports

moleculesmolecules

Molecules to visualize

pdb_datafile

PDB file data

Output Ports

viewer_htmlhtml

HTML viewer component

snapshotimage

Static image snapshot

ProLIF Interaction Analysis

Protein-ligand interaction fingerprint analysis and visualization

Type: prolif_interactionCategory: Molecular Analysis

Key Features

  • •Comprehensive interaction detection
  • •Hydrogen bond analysis
  • •Hydrophobic interaction mapping
  • •Interaction fingerprint generation
  • •Comparative analysis

Input Ports

protein_moleculesmolecules

Protein structure

ligand_moleculesmolecules

Ligand molecules

Output Ports

interaction_datadata

Interaction fingerprint data

interaction_plotimage

Interaction visualization

summary_reportdata

Analysis summary

Statistical Plotting Nodes

20+ plotting nodes for creating publication-ready statistical visualizations.

Histogram Plot

Create histogram plots for data distribution analysis

Statistical Plots
Features:
  • Multiple column support
  • Customizable bin count
  • Density curve overlay
  • Statistical annotations
  • Publication-ready styling

Scatter Plot

Generate scatter plots for correlation and relationship analysis

Statistical Plots
Features:
  • Color mapping by category
  • Size scaling by value
  • Trend line fitting
  • Correlation coefficient display
  • Interactive tooltips

Heatmap Plot

Create heatmap visualizations for correlation matrices and 2D data

Statistical Plots
Features:
  • Color map customization
  • Annotation display
  • Clustering options
  • Dendrogram support
  • Interactive exploration

Complete Plotting Library

VERA includes 20+ plotting nodes covering all major chart types:

Histogram
Scatter Plot
Line Chart
Bar Chart
Pie Chart
Heatmap
Box Plot
Violin Plot
KDE Plot
Area Chart
Bubble Chart
Radar Chart
Stacked Bar
Hist2D
Pair Plot
Volcano Plot
Venn Diagram
ECDF
Hexbin
Error Bar