Multi-quantitative tracks

JBrowse can show "Multi-quantitative tracks" which is a single track composed of multiple quantitative signals, which have their Y-scalebar synchronized.

There are 5 rendering modes for the multi-quantitative tracks.

  • xyplot
  • multirowxyplot
  • multiline
  • multirowline
  • multidensity

You can interactively change these settings through the track menu.

Track menu for the multi-quantitative tracks showing different renderer types.
Track menu for the multi-quantitative tracks showing different renderer types.

With the "multi-row" settings (multirowxyplot, multirowline, multidensity) the track colors are not modified. For the overlapping (xyplot, multiline), the tracks will be autoassigned a color from the palette. You can manually customize the subtrack colors from the track menu as well.

The color/arrangement editor for multi-quantitative tracks lets you change individual subtrack colors, or their ordering in the row based layouts.
The color/arrangement editor for multi-quantitative tracks lets you change individual subtrack colors, or their ordering in the row based layouts.

Oftentimes, one of the outliers on one of the subtracks may affect the Y-scalebar too much, so it is often helpful to use the "Autoscale type → Local +/- 3SD" setting (3 standard deviations are displayed). Manually configuring the min or max scores is available via the track menu also.

Adding multi-quantitative tracks via the UI

There are several ways to create multi-quantitative tracks from scratch.

  1. Using the add track panel to open up a list of URLs for bigwig files, or from several local tracks from your machine
  2. Using the track selector to add multiple tracks to your current selection, and then creating a multi-wiggle track from the tracks in your selection
  3. Hardcoding the multiwiggle track in your config file (see multi-quantitative track configuration for more info)
Using the add track widget, you can use the select dropdown to access alternative 'add track workflows' including the multi-wiggle add track workflow. In the multiwiggle add track workflow, you can paste a list of bigWig file URLs, or open up multiple bigwig files from your computer.
Using the add track widget, you can use the select dropdown to access alternative 'add track workflows' including the multi-wiggle add track workflow. In the multiwiggle add track workflow, you can paste a list of bigWig file URLs, or open up multiple bigwig files from your computer.

Loading bedMethyl as a multi-quantitative track

modkit pileup produces a bedMethyl file — a tab-separated BED format where each row reports the methylation fraction at a single CpG position for one modification type (e.g. 5mC or 5hmC). Because the format is a BED file it can be loaded with BedTabixAdapter, and because each modification type produces its own score column the file maps naturally to a MultiQuantitativeTrack.

Generating the file

modkit pileup sample.bam output.bed --ref reference.fa --preset traditional
bgzip output.bed
tabix -p bed output.bed.gz

The --preset traditional flag produces 5mC calls (5hmC is combined into the 5mC fraction). Omit it for separate 5mC and 5hmC rows.

Add-track UI

In the add-track dialog (File → Open track...), paste the URL to your .bedmethyl.gz file. JBrowse detects the .bedmethyl.gz extension and automatically selects BedTabixAdapter and MultiQuantitativeTrack — no manual selection needed.

Config example

{
  "type": "MultiQuantitativeTrack",
  "trackId": "sample_modkit",
  "name": "CpG methylation (modkit)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "BedTabixAdapter",
    "bedGzLocation": {
      "uri": "https://yourhost/sample_modkit.bed.gz"
    },
    "index": {
      "location": {
        "uri": "https://yourhost/sample_modkit.bed.gz.tbi"
      }
    }
  }
}

JBrowse reads the score column (column 11 in bedMethyl, the methylation fraction 0–1) and the name column (column 4, the modification code such as m for 5mC or h for 5hmC) as the subtrack source label.

The COLO829 tumor modkit bedMethyl file is included in the demo config as the track "COLO829_tumor.ht_modkit.bed (as MultiQuantitativeTrack)" under the Methylation category (assembly hg38, chr21).