chromoMap2 App

HOW IT WORKS

Create a chromoMap Plot in three steps

Data

Enter input data using one of the options provided below.

chromoMap2 Features

Visualise feature-associated numerical or categorical data as heatmaps, bar, scatter, line, and other plots. Start in Visualise Data, configure the map in Plot Properties, and explore special plot features in Additional Features.

Create chromoMaps

Build the configured map using the Create chromoMap button in the status bar below.

Project nameSaved projects

Visualise data

Visualize omics data on genomic coordinates for each chromosome set.

Options are applied per chromosome set

Use the selector below to choose the set whose visualization you want to edit.

Chromosome set to edit

Data to visualise

Choose one data mode for the selected chromosome set.

Annotations onlyCategoricalNumeric

Heat map

Visualise the selected annotation data as a chromosome heatmap. For color and domain configuration, go to Plot Properties.

Show heat map

Plot type

Available plot types change with the numerical or categorical data selection above.

Plot properties

Configure chromosome geometry, positioning, scales, and text.

Plot title and description

Describe what the values represent so the assistant can interpret them without guessing.

TitleScientific description

Chromosome layout

Control the primary plot geometry and spacing.

Chromosome widthWindow widthCorner curveChromosome gapChromosome-set gapTop marginLeft marginMargin paddingText x-shift

Automatic left marginCenter plotWindow guides

Guide color

Genomic scale

Format coordinate axes. Tick density adjusts automatically to the available width.

Scale modeMajor ticksMinor ticksScale suffixY scale offset

Typography

Set text sizes used throughout the map.

Chromosome textTitleAxisLegendTooltip

Plot y-axis label config

Position and size labels beside numeric plots.

Y-label x offsetY-label y offsetY-label size

Legend positioning

Position global plot legends and chromoLinks legends.

Links legend xLinks legend yPlot legend xPlot legend yLegend position

Per-set properties

Changes below affect only the selected chromosome set.

Chromosome set to edit

Numeric domain

Choose whether numeric limits are calculated together or per chromosome set.

Numeric domain scope

chromoLinks

Connect annotations and loci across chromosomes or chromosome sets.

Link data

Paste JSON, import a CSV/TSV table, or build links from the annotations already loaded.

Loci links JSON array

Import loci links CSV/TSV

Link appearance

Configure shape, direction, and color mapping.

Show linksDirected edgesChord linksNumeric color map

Export

Download the current plot, an editable HTML project, or its window-level data.

Plot image

These actions use chromoMap2’s built-in export engine.

File namePNG scale

Standalone HTML plot

Export an interactive HTML figure containing the data and configuration. Choose online libraries for a single-file download, or local libraries for offline viewing.

Choose how the HTML will openWith internet: select Online libraries and download just the HTML. Without internet: select Local libraries and download the HTML plus d3.v5.js and chromoMap2.js using the buttons below. Keep all three files together in the same folder.

HTML dependency modeDownload d3.v5.js Download chromoMap2.js

Window data

Export computed chromosome-window summaries as CSV.

Generate a plot firstExport actions become available after chromoMap2 renders.

Generated code

Copy the current configuration into a chromoMap2 project.

OUTPUT

My chromoMap2 plot

Click anywhere above to edit the title/text. Drag plot legends to reposition them.

Your chromoMap2 interactive visualization will appear here

Select one of the methods under Select Data tab to get started.

chromoMap2

A platform for comparative multi-omics visualization across multi-scale genomic landscapes.

Your chromoMap2 interactive visualization will appear here

DATA & PRIVACY POLICY