chromoMap 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

Select data

Start a new plot or import an editable chromoMap HTML project.

Create from data files

Upload chromosome and annotation CSV/TSV tables for each ploidy.

Number of ploidies

Required columnsChromosomes: name, start, end. Annotations: name, ch_name, ch_start, ch_end.

Edit an existing chromoMap

Import embedded data and configuration from a standalone HTML plot.

Import chromoMap HTMLDefaults are restored before imported settings are applied.

Start from an example

Load a ready-to-edit dataset and configuration. Example HTML files from the app’s main directory appear here automatically.

Finding HTML examples…

Visualise data

Visualize omics data on genomic coordinates for each ploidy.

Options are applied per ploidy

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

Ploidy to edit

Data to visualise

Choose one data mode for the selected ploidy.

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

The title displayed above the generated chromosome map.

Title

Chromosome layout

Control the primary plot geometry and spacing.

Chromosome widthWindow widthCorner curveChromosome gapPloidy gapTop marginLeft marginMargin paddingText x-shift

Automatic left marginCenter plotWindow guides

Guide color

Genomic scale

Format coordinate axes and tick marks.

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-ploidy properties

Changes below affect only the selected ploidy.

Ploidy to edit

Numeric domain

Choose whether numeric limits are calculated together or per ploidy.

Numeric domain scope

Additional features

Fine-tune resolution and add genomic context.

Map resolution

Choose adaptive or fixed genomic windows.

Adaptive windowsFixed size

Window factorWindow size (bp)

Remove partial last windowShow window summariesMap spanning annotations

Plot highlights

Shade selected genomic regions behind or above the map.

Highlights JSON array

Import highlights CSV/TSVHighlight layer

Labelling

Display all annotation names or a selected subset.

Annotation labelsOnly label these names comma-separated; blank = all

Max labels/windowLabel fontAngleLabel separator

Strand arrows

Show annotation direction using strand-aware arrows.

Enable strand arrows

Arrow placementArrow colorArrow sizeArrow tail

Markers

Place markers above selected annotations.

Feature names comma-separated

SizeY offsetStroke

Add Text

Add custom text directly to the plot SVG. Drag it on the plot to reposition it; the text is included in PNG and SVG exports.

TextColorSizeRotation

Italic text

Custom legends

Add independent categorical or numeric legends. These legends are global and are not tied to a ploidy.

chromoLinks

Connect annotations and loci across chromosomes or ploidies.

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

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

The exported HTML contains your data and configuration. Keep its two JavaScript dependencies in the same folder so it can render without this app.

Required dependenciesd3.v5.js and chromoMap2.js

Download 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

Scroll horizontally for large genomes

Your chromosome map will appear here

Select data files or import an existing chromoMap HTML project.