Visualizations
Full reference
Every visualization type EMET supports, grouped by category, with what each is best used for and the data it requires. Click the Visualization header to sort alphabetically.
| Visualization | Best used for | Data required |
|---|---|---|
| Genomics & Sequencing | ||
| Manhattan Plot | GWAS results across chromosomes | Chromosome, position, p-value per variant |
| Circos Plot | Circular genome views, fusions, structural variants | Chromosomal coordinates, chord connections |
| Genome Browser | Multi-track interactive genomic region views | Genomic coordinates, track data |
| Primer/Amplicon Viewer | ePCR primer binding sites and amplicons | Primer sequences, genomic coordinates |
| Expression & DE Analysis | ||
| Volcano Plot | Fold change vs. statistical significance | log2FC and p-value per gene |
| MA Plot | DE quality control, expression-dependent bias | A-value (mean) and M-value (log FC) |
| Heatmap | Gene expression matrices, correlation maps | Matrix of numeric values (rows × columns) |
| Box Plot | Distribution comparisons across groups | Numeric values with group labels |
| PCA Plot | Sample clustering, batch effect detection | Pre-computed PC1/PC2 coordinates |
| Horizon Plot | Compact multi-series time courses | Time-series values per series |
| Protein & Structural Biology | ||
| 3D Molecule Viewer | AlphaFold/PDB structures with mutation highlights | UniProt accession or PDB ID |
| MSA Viewer | Multiple sequence alignment with conservation | Pre-aligned sequences (same length, gaps as -) |
| Phylogenetic Tree | Evolutionary relationships with branch lengths | Tree nodes with parent IDs and branch lengths |
| Subcellular Location | Protein localization within cell compartments | UniProt accession, location annotations |
| Mutation Gram (Lollipop) | Hotspot positions across protein domains | Mutation positions, counts, types |
| Drug Discovery & Chemistry | ||
| ADMET Radar Chart | Drug-likeness profiling (Lipinski, Veber) | MW, LogP, HBA, HBD, TPSA, rotatable bonds |
| SAR Viewer | Structure-activity relationships | SMILES + activity values per compound |
| Scaffold Analysis | Murcko scaffold extraction, R-group decomposition | SMILES strings for compound series |
| MMP Viewer | Matched molecular pair transformation analysis | SMILES + activity values per compound |
| Molecular Comparison | MCS highlighting, Tanimoto similarity | 2-4 SMILES strings |
| Substructure Highlight | SMARTS/SMILES pattern in compound grid | SMILES + SMARTS or SMILES substructure |
| Similarity Matrix | Pairwise Tanimoto structural similarity | SMILES strings for compound set |
| 2D Structure Viewer | Single compound 2D depiction | SMILES, InChI, or Molblock |
| Structure Editor (Ketcher) | Interactive molecule drawing and editing | Optional: initial SMILES to load |
| Networks & Pathways | ||
| Network Graph | PPI networks, drug-gene interactions | Nodes and edges (from STRING, SIGNOR, DGIdb, etc.) |
| Hierarchical Edge Bundling | Cross-category connections (kinase families, pathway crosstalk) | Hierarchical nodes with dot-notation IDs |
| Arc Diagram | Linear network for sequential interactions | Ordered nodes and links |
| Sankey Diagram | Flow between stages (patient pathways, drug metabolism) | Source, target, and flow value per link |
| Clinical & Epidemiology | ||
| Kaplan-Meier Curve | Time-to-event survival analysis | Time, events, at-risk counts per group |
| Forest Plot | Meta-analysis effect sizes with CIs | Estimate, lower CI, upper CI per study |
| General Scientific Charts | ||
| Bar Chart | Category comparisons (expression, counts) | Category labels and numeric values |
| Line Chart | Time-series and sequential data | Time points and numeric values per series |
| Scatter Plot | Correlations and clustering | X and Y numeric values per point |
| Histogram | Value distributions (VAF, quality scores) | Array of numeric values |
| Pie Chart | Proportional composition (max 8 categories) | Category labels and values |
| Hierarchical & Categorical | ||
| Treemap | GO terms, pathway category sizes | Hierarchical nodes with leaf values |
| Packed Bubble Chart | Relative magnitudes by category | Nodes with size values and group labels |
| Hierarchical Tree | Disease ontology, GO hierarchy, taxonomy | Nodes with parent IDs |
| Causal Flow Graph | Complex DAG workflows, Mendelian randomization | Skills by category, data flow connections |
| Expression Atlases | ||
| Tissue Expression Anatomogram | Tissue-level gene expression across organs | UBERON tissue IDs with TPM values |
| Protein Atlas Image Viewer | IHC, IF, and pathology images from HPA | HPA image URLs and metadata |
| Literature & Evidence | ||
| OpenI Figure Viewer | Published figures from PubMed Central | PMC IDs and figure image URLs |
| BenchSci Figure Viewer | Experimental reagent figures from literature | BenchSci figure IDs and image URLs |
| Reports & Dashboards | ||
| HTML Dashboard | Interactive multi-section research dashboards | Any structured data |
| HTML Report | Prose-heavy scientific write-ups | Any structured findings |
| PowerPoint Presentation | Slides for lab meetings, grants, conferences | Slide titles and content |
| Code-Generated | ||
| Custom matplotlib/seaborn | Genome tracks, methylation maps, multi-panel figures | Python-compatible data |
| Custom ggplot2 | Publication-quality statistical graphics | R-compatible data |
| AI-Generated Scientific Image | Visual abstracts, mechanism diagrams, pathway illustrations | Text description / prompt |