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Multi-quantitative track

TL;DR: A multi-quantitative track combines several quantitative signals (typically BigWig files) into one track with a shared Y axis. The track menu's Plot type submenu groups the modes by layout:

  • Multi-row (XY plot, Density, Line (step), Line (interpolated), Scatter) draws one plot per subtrack, stacked
  • Overlapping (XY plot, Line (step), Line (interpolated), Scatter) draws all subtracks together
The track menu lists the available plot types. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses volvox, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “MultiWig”.
  3. Type your region of interest into the location box and press Enter.This figure is at ctgA:1-50000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A1-50000%22%2C%22tracks%22%3A%5B%22volvox_microarray_multi%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiwig%2Fmulti_renderer_types

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1-50000",
      "tracks": [
        "volvox_microarray_multi"
      ]
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:1-50000",
)

view.add_track({
    "type": "MultiQuantitativeTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "MultiWiggleAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1-50000",
      "tracks": [
        "volvox_microarray_multi"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Multi-row modes keep each subtrack's configured color. Overlapping modes auto-assign colors from the palette. Edit colors and ordering from the track menu.

An outlier on one subtrack can blow out the shared Y axis. The "Local ± 3σ" autoscale type clips to three standard deviations of the visible data for a more readable view, or pin the min and max from the track menu.

Twelve per-cell-type BigWigs from a 5k PBMC scATAC dataset as one multi-quantitative track, over CD8A and MS4A1 in one discontinuous view. CD8A is carried by the CD8, MAIT and NK rows and MS4A1 by the two B rows, on one shared scale. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq (GFF3Tabix)”.
  3. Track menu → Set feature height → Compact“NCBI RefSeq (GFF3Tabix)”.
  4. Track menu → Show only genes (checked)“NCBI RefSeq (GFF3Tabix)”.
  5. Drag the bar at the bottom edge of the track to resize it.“NCBI RefSeq (GFF3Tabix)”.
  6. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Single-cell ATAC pseudobulk by cell type (10x 5k PBMC, SnapATAC2)”.
  7. Drag the bar at the bottom edge of the track to resize it.“Single-cell ATAC pseudobulk by cell type (10x 5k PBMC, SnapATAC2)”.
  8. Type your region of interest into the location box and press Enter.This figure is at chr2:86,780,000-86,820,000 chr11:60,450,000-60,490,000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr2%3A86%2C780%2C000-86%2C820%2C000+chr11%3A60%2C450%2C000-60%2C490%2C000%22%2C%22type%22%3A%22LinearGenomeView%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_109_hg38_latest%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22displayMode%22%3A%22compact%22%2C%22showOnlyGenes%22%3Atrue%2C%22height%22%3A80%7D%2C%7B%22trackId%22%3A%22pbmc5k_scatac_pseudobulk_hg38%22%2C%22type%22%3A%22MultiLinearWiggleDisplay%22%2C%22height%22%3A300%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+scatac%2Fpbmc5k_marker_swap

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "assembly": "hg38",
      "loc": "chr2:86,780,000-86,820,000 chr11:60,450,000-60,490,000",
      "type": "LinearGenomeView",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "displayMode": "compact",
          "showOnlyGenes": true,
          "height": 80
        },
        {
          "trackId": "pbmc5k_scatac_pseudobulk_hg38",
          "type": "MultiLinearWiggleDisplay",
          "height": 300
        }
      ]
    }
  ]
}

Loaded against config: test_data/config_demo.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg38"),
    location="chr2:86,780,000-86,820,000 chr11:60,450,000-60,490,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "Gff3TabixAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "MultiQuantitativeTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "MultiWiggleAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "assembly": "hg38",
      "loc": "chr2:86,780,000-86,820,000 chr11:60,450,000-60,490,000",
      "type": "LinearGenomeView",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "displayMode": "compact",
          "showOnlyGenes": true,
          "height": 80
        },
        {
          "trackId": "pbmc5k_scatac_pseudobulk_hg38",
          "type": "MultiLinearWiggleDisplay",
          "height": 300
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Adding a multi-quantitative track

Three ways to create one:

  • The "Add a track" form lets you paste a list of BigWig URLs, or open multiple BigWig files from your machine
  • The track selector lets you multi-select existing tracks and combine them into a multi-quantitative track, which is how a set of per-cell-type BigWigs becomes one stacked track (see the single-cell ATAC pseudobulk tutorial)
  • Hand-edit the config, described in the multi-quantitative track configuration guide
The 'Add a track' form's workflow selector (red callout) lets you reach the multi-quantitative workflow, where you can paste a list of BigWig URLs or open multiple BigWig files from disk. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses volvox, loaded from a .2bit genome.
  2. Type your region of interest into the location box and press Enter.This figure is at ctgA:1-20000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A1-20000%22%7D%5D%7D&sessionName=JBrowse+docs%3A+multiwig%2Faddtrack

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1-20000"
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:1-20000",
)

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1-20000"
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

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). It loads as BedTabixAdapter and naturally maps to MultiQuantitativeTrack, with one subtrack per modification type; see Loading bedMethyl as a multi-quantitative track for generating the file and the adapter config. For the per-read view of the same modified-base calls, see Color by base modifications on the alignments track.

Clustering rows by score

Reorder subtracks by signal similarity, via Clustering → Cluster rows by score... in the track menu. Auto mode samples signal values at each pixel across the visible region to build the matrix. See Clustering rows for the modes, the dendrogram, and how to share a result in a session URL.

Clustering a multi-quantitative track. Top: the 'Cluster rows by score' dialog with its auto/manual mode options. Bottom: after clustering, rows are reordered by signal similarity. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “PUR copy number (1000 Genomes)”.
  3. Drag the bar at the bottom edge of the track to resize it.
  4. Track menu → Plot type → Multi-row → Density
  5. Track menu → Score → Autoscale type → Local
  6. Track menu → Show... → Show tree (unchecked)On by default. The item is disabled until there is a tree to show, and drops out entirely in the overlay plot types, which collapse every source onto one row for a dendrogram to align to.
  7. Type your region of interest into the location box and press Enter.This figure is at chr3:162,275,163-163,360,944.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr3%3A162%2C275%2C163-163%2C360%2C944%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22pur_copynumber_1000g%22%2C%22type%22%3A%22MultiLinearWiggleDisplay%22%2C%22height%22%3A420%2C%22defaultRendering%22%3A%22multirowdensity%22%2C%22autoscale%22%3A%22local%22%2C%22showTree%22%3Afalse%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiwig%2Fcluster_dialog

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr3:162,275,163-163,360,944",
      "tracks": [
        {
          "trackId": "pur_copynumber_1000g",
          "type": "MultiLinearWiggleDisplay",
          "height": 420,
          "defaultRendering": "multirowdensity",
          "autoscale": "local",
          "showTree": false
        }
      ]
    }
  ]
}

Loaded against config: test_data/config_demo.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg38"),
    location="chr3:162,275,163-163,360,944",
)

view.add_track({
    "type": "MultiQuantitativeTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "MultiWiggleAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr3:162,275,163-163,360,944",
      "tracks": [
        {
          "trackId": "pur_copynumber_1000g",
          "type": "MultiLinearWiggleDisplay",
          "height": 420,
          "defaultRendering": "multirowdensity",
          "autoscale": "local",
          "showTree": false
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Sorting rows by score at one position

Right-click a multi-row plot at the column you want to rank on and choose Sort rows by score here. The subtracks are reordered by the score each carries at that base, highest at the top, so a cohort reads top-to-bottom at a candidate locus. Clustering orders the rows by the whole region in view; this orders them by a single column.

Reset row order puts the subtracks back in the order they were loaded in. It appears in the same right-click menu and in the track menu, and it undoes a sort, a clustering run, and a hand-arranged order alike.

A session can bake the sort in with sortRowsBy, the way runClustering bakes in a clustering run — see MultiLinearWiggleDisplay for both fields.

See also