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Grouping and lane order

Several unrelated-looking track settings — a gene track's biotype sections, an alignments track's haplotype bands, a multi-sample variant track's karyotype rows, a multiway synteny track's lanes, a multi-row display's partitions — read the same two ideas: a field (or, for multiway synteny, the assembly itself) decides what gets its own section, and a domain list decides which section draws first. This page is the shared mechanism; each example below links to the guide or tutorial it is worked through in full.

field and domain

Most of these displays take a facet object: { field, domain }. field is a feature attribute, a dotted path into a structured one (INFO.SVTYPE), or a jexl: expression — whatever value it returns gets its own section. domain is a list of values: the ones it names stack first, in that order, and every other value found in the data follows, sorted. A value in domain that the data never produces is simply never drawn — domain orders sections, it does not create them, so naming one ahead of time costs nothing and refetches nothing when it later appears.

A short form exists for the common case of no ordering: "facet": "tags.HP" is "facet": { "field": "tags.HP", "domain": [] }.

Feature tracks

NCBI RefSeq genes on hg38, grouped and colored by gene_biotype, with the protein-coding section pinned to the top and each biotype given a distinct color from the same domain:

{
  "facet": {
    "field": "gene_biotype",
    "domain": ["protein_coding", "snoRNA", "lncRNA", "pseudogene"]
  },
  "color": {
    "field": "gene_biotype",
    "domain": ["protein_coding", "snoRNA", "lncRNA", "pseudogene"]
  }
}
NCBI RefSeq genes on hg38: Edit as JSON from the Group by dialog, the spec above pasted in, and the sections stacked in the facet's domain order, each biotype colored by its position in the color's domain. Open the session this video starts in ↗

Open the session the video starts in ↗, then take the steps it shows:

  1. Write the grouping as JSON from the Group by dialog
  2. A facet and a color, each with its domain
  3. Sections and colors follow each domain

The track the video adds through the form, as the page above prints it:

{
  "facet": {
    "field": "gene_biotype",
    "domain": ["protein_coding", "snoRNA", "lncRNA", "pseudogene"]
  },
  "color": {
    "field": "gene_biotype",
    "domain": ["protein_coding", "snoRNA", "lncRNA", "pseudogene"]
  }
}

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

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%22chr17%3A7%2C540%2C000-7%2C640%2C000%22%2C%22trackLabels%22%3A%22offset%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_109_hg38_latest%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22showLabels%22%3A%22name%22%2C%22height%22%3A640%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+ui%2Fgene_track_channel_spec

With your own data, the steps behind the figure:

  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)”.
    1. Track menu → Gene glyph → Representative transcript
    2. Track menu → Show... → Labels → Name only
    3. Drag the bar at the bottom edge of the track to resize it (640px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr17:7,540,000-7,640,000.
  4. View menu → Show... → Offset

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.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)”.
    1. Track menu → Gene glyph → Representative transcript
    2. Track menu → Show... → Labels → Name only
    3. Drag the bar at the bottom edge of the track to resize it (640px here).
  3. Type your region of interest into the location box and press Enter.This figure is at chr17:7,540,000-7,640,000.
  4. View menu → Show... → Offset

This session spec draws the figure from test_data/config_demo.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr17:7,540,000-7,640,000",
      "trackLabels": "offset",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "showLabels": "name",
          "height": 640
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/config_demo.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr17:7,540,000-7,640,000",
            "trackLabels": "offset",
            "tracks": [
                {
                    "trackId": "ncbi_refseq_109_hg38_latest",
                    "type": "LinearBasicDisplay",
                    "geneGlyphMode": "longestCoding",
                    "showLabels": "name",
                    "height": 640
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --assembly hg38 --loc chr17:7,540,000-7,640,000 \
  --trackLabels offset \
  --track ncbi_refseq_109_hg38_latest display:LinearBasicDisplay '{"geneGlyphMode":"longestCoding","showLabels":"name","height":640}' \
  --width 1920 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

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": "chr17:7,540,000-7,640,000",
      "trackLabels": "offset",
      "tracks": [
        {
          "trackId": "ncbi_refseq_109_hg38_latest",
          "type": "LinearBasicDisplay",
          "geneGlyphMode": "longestCoding",
          "showLabels": "name",
          "height": 640
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --width 1920 --height 740 \
  --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.

The gene track guide's Grouping features into sections section has the full mechanism — the Group by/Color by dialogs, the Sections menu, and what Edit as JSON... accepts.

Alignments tracks

The alignments displays take facet the same way, plus a handful of read dimensions no attribute expresses — strand, firstOfPairStrand, pairOrientation, splitRead, mapq. The same idea over a LinearMarkDisplay faceting a BAM by its HP haplotype tag:

HG002 ONT reads faceted by their HP tag: each haplotype's reads packed into a separate band under the chip that names it, and the untagged reads in a third. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

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%22sessionTracks%22%3A%5B%7B%22type%22%3A%22AlignmentsTrack%22%2C%22trackId%22%3A%22snrpn_facet%22%2C%22name%22%3A%22HG002+ONT+reads+faceted+by+HP%22%2C%22assemblyNames%22%3A%5B%22hg38%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BamAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fmethylation%2FHG002_SNRPN_5mC_haplotagged.bam%22%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearMarkDisplay%22%2C%22displayId%22%3A%22snrpn_facet-LinearMarkDisplay%22%2C%22transform%22%3A%5B%7B%22type%22%3A%22formula%22%2C%22expr%22%3A%22jexl%3AgetTag%28feature%2C%27HP%27%29%22%2C%22as%22%3A%22HP%22%7D%5D%2C%22facet%22%3A%22HP%22%2C%22marks%22%3A%5B%7B%22mark%22%3A%22span%22%2C%22transform%22%3A%5B%7B%22type%22%3A%22pileup%22%7D%5D%2C%22encoding%22%3A%7B%22row%22%3A%22row%22%2C%22color%22%3A%7B%22field%22%3A%22HP%22%2C%22scale%22%3A%22categorical%22%2C%22title%22%3A%22Haplotype%22%7D%7D%7D%5D%7D%5D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr15%3A24%2C900%2C000-25%2C000%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22snrpn_facet%22%2C%22type%22%3A%22LinearMarkDisplay%22%2C%22height%22%3A400%2C%22forceLoad%22%3Atrue%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+mark_display%2Ffacet

With your own data, the steps behind the figure:

  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 BAM file (.bam + .bai).This figure uses “HG002 ONT reads faceted by HP”.
    1. Drag the bar at the bottom edge of the track to resize it (400px here).
    2. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.
  3. Type your region of interest into the location box and press Enter.This figure is at chr15:24,900,000-25,000,000.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.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 BAM file (.bam + .bai).This figure uses “HG002 ONT reads faceted by HP”.
    1. Drag the bar at the bottom edge of the track to resize it (400px here).
    2. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.
  3. Type your region of interest into the location box and press Enter.This figure is at chr15:24,900,000-25,000,000.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "AlignmentsTrack",
  "trackId": "snrpn_facet",
  "name": "HG002 ONT reads faceted by HP",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "BamAdapter",
    "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "displayId": "snrpn_facet-LinearMarkDisplay",
      "transform": [
        {
          "type": "formula",
          "expr": "jexl:getTag(feature,'\''HP'\'')",
          "as": "HP"
        }
      ],
      "facet": "HP",
      "marks": [
        {
          "mark": "span",
          "transform": [
            {
              "type": "pileup"
            }
          ],
          "encoding": {
            "row": "row",
            "color": {
              "field": "HP",
              "scale": "categorical",
              "title": "Haplotype"
            }
          }
        }
      ]
    }
  ]
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs hg38 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/config_demo.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "AlignmentsTrack",
      "trackId": "snrpn_facet",
      "name": "HG002 ONT reads faceted by HP",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "BamAdapter",
        "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
      },
      "displays": [
        {
          "type": "LinearMarkDisplay",
          "displayId": "snrpn_facet-LinearMarkDisplay",
          "transform": [
            {
              "type": "formula",
              "expr": "jexl:getTag(feature,'HP')",
              "as": "HP"
            }
          ],
          "facet": "HP",
          "marks": [
            {
              "mark": "span",
              "transform": [
                {
                  "type": "pileup"
                }
              ],
              "encoding": {
                "row": "row",
                "color": {
                  "field": "HP",
                  "scale": "categorical",
                  "title": "Haplotype"
                }
              }
            }
          ]
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr15:24,900,000-25,000,000",
      "tracks": [
        {
          "trackId": "snrpn_facet",
          "type": "LinearMarkDisplay",
          "height": 400,
          "forceLoad": true
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/config_demo.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "AlignmentsTrack",
            "trackId": "snrpn_facet",
            "name": "HG002 ONT reads faceted by HP",
            "assemblyNames": [
                "hg38"
            ],
            "adapter": {
                "type": "BamAdapter",
                "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
            },
            "displays": [
                {
                    "type": "LinearMarkDisplay",
                    "displayId": "snrpn_facet-LinearMarkDisplay",
                    "transform": [
                        {
                            "type": "formula",
                            "expr": "jexl:getTag(feature,'HP')",
                            "as": "HP"
                        }
                    ],
                    "facet": "HP",
                    "marks": [
                        {
                            "mark": "span",
                            "transform": [
                                {
                                    "type": "pileup"
                                }
                            ],
                            "encoding": {
                                "row": "row",
                                "color": {
                                    "field": "HP",
                                    "scale": "categorical",
                                    "title": "Haplotype"
                                }
                            }
                        }
                    ]
                }
            ]
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr15:24,900,000-25,000,000",
            "tracks": [
                {
                    "trackId": "snrpn_facet",
                    "type": "LinearMarkDisplay",
                    "height": 400,
                    "forceLoad": True
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

cat > tracks.json <<'JSON'
[
  {
    "type": "AlignmentsTrack",
    "trackId": "snrpn_facet",
    "name": "HG002 ONT reads faceted by HP",
    "assemblyNames": [
      "hg38"
    ],
    "adapter": {
      "type": "BamAdapter",
      "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
    },
    "displays": [
      {
        "type": "LinearMarkDisplay",
        "displayId": "snrpn_facet-LinearMarkDisplay",
        "transform": [
          {
            "type": "formula",
            "expr": "jexl:getTag(feature,'HP')",
            "as": "HP"
          }
        ],
        "facet": "HP",
        "marks": [
          {
            "mark": "span",
            "transform": [
              {
                "type": "pileup"
              }
            ],
            "encoding": {
              "row": "row",
              "color": {
                "field": "HP",
                "scale": "categorical",
                "title": "Haplotype"
              }
            }
          }
        ]
      }
    ]
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --tracks tracks.json \
  --assembly hg38 --loc chr15:24,900,000-25,000,000 \
  --track snrpn_facet display:LinearMarkDisplay '{"height":400,"forceLoad":true}' \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

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'
{
  "sessionTracks": [
    {
      "type": "AlignmentsTrack",
      "trackId": "snrpn_facet",
      "name": "HG002 ONT reads faceted by HP",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "BamAdapter",
        "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
      },
      "displays": [
        {
          "type": "LinearMarkDisplay",
          "displayId": "snrpn_facet-LinearMarkDisplay",
          "transform": [
            {
              "type": "formula",
              "expr": "jexl:getTag(feature,'HP')",
              "as": "HP"
            }
          ],
          "facet": "HP",
          "marks": [
            {
              "mark": "span",
              "transform": [
                {
                  "type": "pileup"
                }
              ],
              "encoding": {
                "row": "row",
                "color": {
                  "field": "HP",
                  "scale": "categorical",
                  "title": "Haplotype"
                }
              }
            }
          ]
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr15:24,900,000-25,000,000",
      "tracks": [
        {
          "trackId": "snrpn_facet",
          "type": "LinearMarkDisplay",
          "height": 400,
          "forceLoad": true
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --width 1500 --height 610 \
  --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.

The cookbook's alignments recipe has a worked LinearAlignmentsDisplay config; the reordering rule is the same domain.

Variant tracks

LinearMultiSampleVariantDisplay takes the same facet object to band rows by a metadata column instead of VCF file order. Bands are what makes two biologically meaningful examples readable rather than a wall of samples in whatever order the VCF lists them:

"facet": { "field": "karyotype", "domain": ["Standard", "In(2L)t"] }
Top: the six dm6 arms with the In(2L)t extent over Fst between the two arrangements; the block on 2L stands against low background elsewhere. Below, a second view of chr2L adds one row per DGRP line, genotyped for the inversion and grouped by karyotype. The carrier block spans breakpoint to breakpoint; the Fst plateau runs past both. Open in JBrowse: Six arms ↗

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fucsc%2Fdm6%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22in2lt_inversion%22%2C%22name%22%3A%22In%282L%29t+inversion%22%2C%22assemblyNames%22%3A%5B%22dm6%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22FromConfigAdapter%22%2C%22adapterId%22%3A%22in2lt%22%2C%22features%22%3A%5B%7B%22uniqueId%22%3A%22in2lt%22%2C%22refName%22%3A%22chr2L%22%2C%22start%22%3A2225744%2C%22end%22%3A13154180%2C%22name%22%3A%22In%282L%29t%22%2C%22type%22%3A%22inversion%22%7D%5D%7D%7D%2C%7B%22type%22%3A%22QuantitativeTrack%22%2C%22trackId%22%3A%22fst_in2lt%22%2C%22name%22%3A%22Fst+%28In%282L%29t+vs+standard%29%22%2C%22assemblyNames%22%3A%5B%22dm6%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BigWigAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Ffst_In2Lt.bw%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22dm6%22%2C%22displayedRegionNames%22%3A%5B%22chr2L%22%2C%22chr2R%22%2C%22chr3L%22%2C%22chr3R%22%2C%22chr4%22%2C%22chrX%22%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22in2lt_inversion%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A40%7D%2C%7B%22trackId%22%3A%22fst_in2lt%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A240%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+popgen%2Ffst_in2lt_2L

With your own data, the steps behind the figure:

  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 dm6, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs features defined inline in the config.This figure uses “In(2L)t inversion”.
    1. Drag the bar at the bottom edge of the track to resize it (40px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “Fst (In(2L)t vs standard)”.
    1. Drag the bar at the bottom edge of the track to resize it (240px here).

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses dm6, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs features defined inline in the config.This figure uses “In(2L)t inversion”.
    1. Drag the bar at the bottom edge of the track to resize it (40px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “Fst (In(2L)t vs standard)”.
    1. Drag the bar at the bottom edge of the track to resize it (240px here).

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "in2lt_inversion",
  "name": "In(2L)t inversion",
  "assemblyNames": [
    "dm6"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "adapterId": "in2lt",
    "features": [
      {
        "uniqueId": "in2lt",
        "refName": "chr2L",
        "start": 2225744,
        "end": 13154180,
        "name": "In(2L)t",
        "type": "inversion"
      }
    ]
  }
}'

jbrowse add-track https://jbrowse.org/demos/popgen/fst_In2Lt.bw \
  --trackId fst_in2lt \
  --name "Fst (In(2L)t vs standard)" \
  --assemblyNames dm6

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs dm6 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from https://jbrowse.org/ucsc/dm6/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "in2lt_inversion",
      "name": "In(2L)t inversion",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "in2lt",
        "features": [
          {
            "uniqueId": "in2lt",
            "refName": "chr2L",
            "start": 2225744,
            "end": 13154180,
            "name": "In(2L)t",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "fst_in2lt",
      "name": "Fst (In(2L)t vs standard)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/fst_In2Lt.bw"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "dm6",
      "displayedRegionNames": [
        "chr2L",
        "chr2R",
        "chr3L",
        "chr3R",
        "chr4",
        "chrX"
      ],
      "tracks": [
        {
          "trackId": "in2lt_inversion",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "fst_in2lt",
          "type": "LinearWiggleDisplay",
          "height": 240
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/ucsc/dm6/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "in2lt_inversion",
            "name": "In(2L)t inversion",
            "assemblyNames": [
                "dm6"
            ],
            "adapter": {
                "type": "FromConfigAdapter",
                "adapterId": "in2lt",
                "features": [
                    {
                        "uniqueId": "in2lt",
                        "refName": "chr2L",
                        "start": 2225744,
                        "end": 13154180,
                        "name": "In(2L)t",
                        "type": "inversion"
                    }
                ]
            }
        },
        {
            "type": "QuantitativeTrack",
            "trackId": "fst_in2lt",
            "name": "Fst (In(2L)t vs standard)",
            "assemblyNames": [
                "dm6"
            ],
            "adapter": {
                "type": "BigWigAdapter",
                "uri": "https://jbrowse.org/demos/popgen/fst_In2Lt.bw"
            }
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "dm6",
            "displayedRegionNames": [
                "chr2L",
                "chr2R",
                "chr3L",
                "chr3R",
                "chr4",
                "chrX"
            ],
            "tracks": [
                {
                    "trackId": "in2lt_inversion",
                    "type": "LinearBasicDisplay",
                    "height": 40
                },
                {
                    "trackId": "fst_in2lt",
                    "type": "LinearWiggleDisplay",
                    "height": 240
                }
            ]
        }
    ],
)
app  # 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'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "in2lt_inversion",
      "name": "In(2L)t inversion",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "in2lt",
        "features": [
          {
            "uniqueId": "in2lt",
            "refName": "chr2L",
            "start": 2225744,
            "end": 13154180,
            "name": "In(2L)t",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "fst_in2lt",
      "name": "Fst (In(2L)t vs standard)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/fst_In2Lt.bw"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "dm6",
      "displayedRegionNames": [
        "chr2L",
        "chr2R",
        "chr3L",
        "chr3R",
        "chr4",
        "chrX"
      ],
      "tracks": [
        {
          "trackId": "in2lt_inversion",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "fst_in2lt",
          "type": "LinearWiggleDisplay",
          "height": 240
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/ucsc/dm6/config.json \
  --width 1500 --height 560 \
  --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.

"facet": { "field": "karyotype", "domain": ["2L+a/2L+a", "2La/2L+a", "2La/2La"] }
Ag1000G chromosome arm 2L, the same window and settings throughout. Top: the published extents of 2La and of Vgsc, the two loci the blocks below sit on. r² fills the 2La extent in the Cameroon panel, which segregates both arrangements, and is empty over that span in Gabon, which is near-fixed for the standard arrangement. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fucsc%2FanoGam3%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22ag1000g_2l_loci%22%2C%22name%22%3A%222L+loci%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22FromConfigAdapter%22%2C%22adapterId%22%3A%22ag1000g_2l_loci%22%2C%22features%22%3A%5B%7B%22uniqueId%22%3A%22vgsc%22%2C%22refName%22%3A%22chr2L%22%2C%22start%22%3A2358158%2C%22end%22%3A2431617%2C%22name%22%3A%22Vgsc%22%2C%22type%22%3A%22gene%22%7D%2C%7B%22uniqueId%22%3A%22two_la%22%2C%22refName%22%3A%22chr2L%22%2C%22start%22%3A20524058%2C%22end%22%3A42165532%2C%22name%22%3A%222La%22%2C%22type%22%3A%22inversion%22%7D%5D%7D%7D%2C%7B%22type%22%3A%22LDTrack%22%2C%22trackId%22%3A%22ag1000g_2l_cmgam%22%2C%22name%22%3A%22Cameroon%2C+both+arrangements+segregating+%28r%C2%B2%29%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22PlinkLDTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2L_CMgam.ld.gz%22%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LDTrackDisplay%22%2C%22ldMetric%22%3A%22r2%22%2C%22variantLayout%22%3A%22genomic%22%2C%22showLegend%22%3Atrue%2C%22squashToHeight%22%3Afalse%2C%22height%22%3A340%7D%5D%7D%2C%7B%22type%22%3A%22VariantTrack%22%2C%22trackId%22%3A%22ag1000g_2la_karyotype_cmgam%22%2C%22name%22%3A%22Cameroon%2C+one+row+per+mosquito%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22VcfTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_CMgam.vcf.gz%22%2C%22samplesTsvLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_CMgam_samples.tsv%22%7D%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22facet%22%3A%7B%22field%22%3A%22karyotype%22%2C%22domain%22%3A%5B%222L%2Ba%2F2L%2Ba%22%2C%222La%2F2L%2Ba%22%2C%222La%2F2La%22%5D%7D%2C%22rowColor%22%3A%22karyotype%22%2C%22referenceDrawingMode%22%3A%22skip%22%2C%22showLegend%22%3Atrue%2C%22height%22%3A200%7D%5D%7D%2C%7B%22type%22%3A%22LDTrack%22%2C%22trackId%22%3A%22ag1000g_2l_gagam%22%2C%22name%22%3A%22Gabon%2C+one+arrangement+in+almost+every+mosquito+%28r%C2%B2%29%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22PlinkLDTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2L_GAgam.ld.gz%22%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LDTrackDisplay%22%2C%22ldMetric%22%3A%22r2%22%2C%22variantLayout%22%3A%22genomic%22%2C%22showLegend%22%3Atrue%2C%22squashToHeight%22%3Afalse%2C%22height%22%3A250%7D%5D%7D%2C%7B%22type%22%3A%22VariantTrack%22%2C%22trackId%22%3A%22ag1000g_2la_karyotype_gagam%22%2C%22name%22%3A%22Gabon%2C+one+row+per+mosquito%22%2C%22assemblyNames%22%3A%5B%22anoGam3%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22VcfTabixAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_GAgam.vcf.gz%22%2C%22samplesTsvLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fag1000g_2La_GAgam_samples.tsv%22%7D%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearMultiSampleVariantDisplay%22%2C%22facet%22%3A%7B%22field%22%3A%22karyotype%22%2C%22domain%22%3A%5B%222L%2Ba%2F2L%2Ba%22%2C%222La%2F2L%2Ba%22%2C%222La%2F2La%22%5D%7D%2C%22rowColor%22%3A%22karyotype%22%2C%22referenceDrawingMode%22%3A%22skip%22%2C%22showLegend%22%3Afalse%2C%22height%22%3A170%7D%5D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22anoGam3%22%2C%22loc%22%3A%22chr2L%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ag1000g_2l_loci%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A40%7D%2C%7B%22trackId%22%3A%22ag1000g_2l_cmgam%22%2C%22type%22%3A%22LDTrackDisplay%22%7D%2C%7B%22trackId%22%3A%22ag1000g_2la_karyotype_cmgam%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%7D%2C%7B%22trackId%22%3A%22ag1000g_2l_gagam%22%2C%22type%22%3A%22LDTrackDisplay%22%7D%2C%7B%22trackId%22%3A%22ag1000g_2la_karyotype_gagam%22%2C%22type%22%3A%22LinearMultiSampleVariantDisplay%22%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+ld%2Fanopheles_2la

With your own data, the steps behind the figure:

  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 anoGam3, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs features defined inline in the config.This figure uses “2L loci”.
    1. Drag the bar at the bottom edge of the track to resize it (40px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Cameroon, both arrangements segregating (r²)”.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “Cameroon, one row per mosquito”.
  5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Gabon, one arrangement in almost every mosquito (r²)”.
  6. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “Gabon, one row per mosquito”.
  7. Type your region of interest into the location box and press Enter.This figure is at chr2L.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses anoGam3, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs features defined inline in the config.This figure uses “2L loci”.
    1. Drag the bar at the bottom edge of the track to resize it (40px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Cameroon, both arrangements segregating (r²)”.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “Cameroon, one row per mosquito”.
  5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Gabon, one arrangement in almost every mosquito (r²)”.
  6. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “Gabon, one row per mosquito”.
  7. Type your region of interest into the location box and press Enter.This figure is at chr2L.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "ag1000g_2l_loci",
  "name": "2L loci",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "adapterId": "ag1000g_2l_loci",
    "features": [
      {
        "uniqueId": "vgsc",
        "refName": "chr2L",
        "start": 2358158,
        "end": 2431617,
        "name": "Vgsc",
        "type": "gene"
      },
      {
        "uniqueId": "two_la",
        "refName": "chr2L",
        "start": 20524058,
        "end": 42165532,
        "name": "2La",
        "type": "inversion"
      }
    ]
  }
}'

jbrowse add-track-json '{
  "type": "LDTrack",
  "trackId": "ag1000g_2l_cmgam",
  "name": "Cameroon, both arrangements segregating (r²)",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "PlinkLDTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
  },
  "displays": [
    {
      "type": "LDTrackDisplay",
      "ldMetric": "r2",
      "variantLayout": "genomic",
      "showLegend": true,
      "squashToHeight": false,
      "height": 340
    }
  ]
}'

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "ag1000g_2la_karyotype_cmgam",
  "name": "Cameroon, one row per mosquito",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "facet": {
        "field": "karyotype",
        "domain": [
          "2L+a/2L+a",
          "2La/2L+a",
          "2La/2La"
        ]
      },
      "rowColor": "karyotype",
      "referenceDrawingMode": "skip",
      "showLegend": true,
      "height": 200
    }
  ]
}'

jbrowse add-track-json '{
  "type": "LDTrack",
  "trackId": "ag1000g_2l_gagam",
  "name": "Gabon, one arrangement in almost every mosquito (r²)",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "PlinkLDTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
  },
  "displays": [
    {
      "type": "LDTrackDisplay",
      "ldMetric": "r2",
      "variantLayout": "genomic",
      "showLegend": true,
      "squashToHeight": false,
      "height": 250
    }
  ]
}'

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "ag1000g_2la_karyotype_gagam",
  "name": "Gabon, one row per mosquito",
  "assemblyNames": [
    "anoGam3"
  ],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "facet": {
        "field": "karyotype",
        "domain": [
          "2L+a/2L+a",
          "2La/2L+a",
          "2La/2La"
        ]
      },
      "rowColor": "karyotype",
      "referenceDrawingMode": "skip",
      "showLegend": false,
      "height": 170
    }
  ]
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs anoGam3 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from https://jbrowse.org/ucsc/anoGam3/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ag1000g_2l_loci",
      "name": "2L loci",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "ag1000g_2l_loci",
        "features": [
          {
            "uniqueId": "vgsc",
            "refName": "chr2L",
            "start": 2358158,
            "end": 2431617,
            "name": "Vgsc",
            "type": "gene"
          },
          {
            "uniqueId": "two_la",
            "refName": "chr2L",
            "start": 20524058,
            "end": 42165532,
            "name": "2La",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_cmgam",
      "name": "Cameroon, both arrangements segregating (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "variantLayout": "genomic",
          "showLegend": true,
          "squashToHeight": false,
          "height": 340
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_cmgam",
      "name": "Cameroon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "facet": {
            "field": "karyotype",
            "domain": [
              "2L+a/2L+a",
              "2La/2L+a",
              "2La/2La"
            ]
          },
          "rowColor": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": true,
          "height": 200
        }
      ]
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_gagam",
      "name": "Gabon, one arrangement in almost every mosquito (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "variantLayout": "genomic",
          "showLegend": true,
          "squashToHeight": false,
          "height": 250
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_gagam",
      "name": "Gabon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "facet": {
            "field": "karyotype",
            "domain": [
              "2L+a/2L+a",
              "2La/2L+a",
              "2La/2La"
            ]
          },
          "rowColor": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": false,
          "height": 170
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "anoGam3",
      "loc": "chr2L",
      "tracks": [
        {
          "trackId": "ag1000g_2l_loci",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "ag1000g_2l_cmgam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_cmgam",
          "type": "LinearMultiSampleVariantDisplay"
        },
        {
          "trackId": "ag1000g_2l_gagam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_gagam",
          "type": "LinearMultiSampleVariantDisplay"
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/ucsc/anoGam3/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "ag1000g_2l_loci",
            "name": "2L loci",
            "assemblyNames": [
                "anoGam3"
            ],
            "adapter": {
                "type": "FromConfigAdapter",
                "adapterId": "ag1000g_2l_loci",
                "features": [
                    {
                        "uniqueId": "vgsc",
                        "refName": "chr2L",
                        "start": 2358158,
                        "end": 2431617,
                        "name": "Vgsc",
                        "type": "gene"
                    },
                    {
                        "uniqueId": "two_la",
                        "refName": "chr2L",
                        "start": 20524058,
                        "end": 42165532,
                        "name": "2La",
                        "type": "inversion"
                    }
                ]
            }
        },
        {
            "type": "LDTrack",
            "trackId": "ag1000g_2l_cmgam",
            "name": "Cameroon, both arrangements segregating (r²)",
            "assemblyNames": [
                "anoGam3"
            ],
            "adapter": {
                "type": "PlinkLDTabixAdapter",
                "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
            },
            "displays": [
                {
                    "type": "LDTrackDisplay",
                    "ldMetric": "r2",
                    "variantLayout": "genomic",
                    "showLegend": True,
                    "squashToHeight": False,
                    "height": 340
                }
            ]
        },
        {
            "type": "VariantTrack",
            "trackId": "ag1000g_2la_karyotype_cmgam",
            "name": "Cameroon, one row per mosquito",
            "assemblyNames": [
                "anoGam3"
            ],
            "adapter": {
                "type": "VcfTabixAdapter",
                "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
                "samplesTsvLocation": {
                    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
                }
            },
            "displays": [
                {
                    "type": "LinearMultiSampleVariantDisplay",
                    "facet": {
                        "field": "karyotype",
                        "domain": [
                            "2L+a/2L+a",
                            "2La/2L+a",
                            "2La/2La"
                        ]
                    },
                    "rowColor": "karyotype",
                    "referenceDrawingMode": "skip",
                    "showLegend": True,
                    "height": 200
                }
            ]
        },
        {
            "type": "LDTrack",
            "trackId": "ag1000g_2l_gagam",
            "name": "Gabon, one arrangement in almost every mosquito (r²)",
            "assemblyNames": [
                "anoGam3"
            ],
            "adapter": {
                "type": "PlinkLDTabixAdapter",
                "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
            },
            "displays": [
                {
                    "type": "LDTrackDisplay",
                    "ldMetric": "r2",
                    "variantLayout": "genomic",
                    "showLegend": True,
                    "squashToHeight": False,
                    "height": 250
                }
            ]
        },
        {
            "type": "VariantTrack",
            "trackId": "ag1000g_2la_karyotype_gagam",
            "name": "Gabon, one row per mosquito",
            "assemblyNames": [
                "anoGam3"
            ],
            "adapter": {
                "type": "VcfTabixAdapter",
                "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
                "samplesTsvLocation": {
                    "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
                }
            },
            "displays": [
                {
                    "type": "LinearMultiSampleVariantDisplay",
                    "facet": {
                        "field": "karyotype",
                        "domain": [
                            "2L+a/2L+a",
                            "2La/2L+a",
                            "2La/2La"
                        ]
                    },
                    "rowColor": "karyotype",
                    "referenceDrawingMode": "skip",
                    "showLegend": False,
                    "height": 170
                }
            ]
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "anoGam3",
            "loc": "chr2L",
            "tracks": [
                {
                    "trackId": "ag1000g_2l_loci",
                    "type": "LinearBasicDisplay",
                    "height": 40
                },
                {
                    "trackId": "ag1000g_2l_cmgam",
                    "type": "LDTrackDisplay"
                },
                {
                    "trackId": "ag1000g_2la_karyotype_cmgam",
                    "type": "LinearMultiSampleVariantDisplay"
                },
                {
                    "trackId": "ag1000g_2l_gagam",
                    "type": "LDTrackDisplay"
                },
                {
                    "trackId": "ag1000g_2la_karyotype_gagam",
                    "type": "LinearMultiSampleVariantDisplay"
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

cat > tracks.json <<'JSON'
[
  {
    "type": "FeatureTrack",
    "trackId": "ag1000g_2l_loci",
    "name": "2L loci",
    "assemblyNames": [
      "anoGam3"
    ],
    "adapter": {
      "type": "FromConfigAdapter",
      "adapterId": "ag1000g_2l_loci",
      "features": [
        {
          "uniqueId": "vgsc",
          "refName": "chr2L",
          "start": 2358158,
          "end": 2431617,
          "name": "Vgsc",
          "type": "gene"
        },
        {
          "uniqueId": "two_la",
          "refName": "chr2L",
          "start": 20524058,
          "end": 42165532,
          "name": "2La",
          "type": "inversion"
        }
      ]
    }
  },
  {
    "type": "LDTrack",
    "trackId": "ag1000g_2l_cmgam",
    "name": "Cameroon, both arrangements segregating (r²)",
    "assemblyNames": [
      "anoGam3"
    ],
    "adapter": {
      "type": "PlinkLDTabixAdapter",
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
    },
    "displays": [
      {
        "type": "LDTrackDisplay",
        "ldMetric": "r2",
        "variantLayout": "genomic",
        "showLegend": true,
        "squashToHeight": false,
        "height": 340
      }
    ]
  },
  {
    "type": "VariantTrack",
    "trackId": "ag1000g_2la_karyotype_cmgam",
    "name": "Cameroon, one row per mosquito",
    "assemblyNames": [
      "anoGam3"
    ],
    "adapter": {
      "type": "VcfTabixAdapter",
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
      "samplesTsvLocation": {
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
      }
    },
    "displays": [
      {
        "type": "LinearMultiSampleVariantDisplay",
        "facet": {
          "field": "karyotype",
          "domain": [
            "2L+a/2L+a",
            "2La/2L+a",
            "2La/2La"
          ]
        },
        "rowColor": "karyotype",
        "referenceDrawingMode": "skip",
        "showLegend": true,
        "height": 200
      }
    ]
  },
  {
    "type": "LDTrack",
    "trackId": "ag1000g_2l_gagam",
    "name": "Gabon, one arrangement in almost every mosquito (r²)",
    "assemblyNames": [
      "anoGam3"
    ],
    "adapter": {
      "type": "PlinkLDTabixAdapter",
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
    },
    "displays": [
      {
        "type": "LDTrackDisplay",
        "ldMetric": "r2",
        "variantLayout": "genomic",
        "showLegend": true,
        "squashToHeight": false,
        "height": 250
      }
    ]
  },
  {
    "type": "VariantTrack",
    "trackId": "ag1000g_2la_karyotype_gagam",
    "name": "Gabon, one row per mosquito",
    "assemblyNames": [
      "anoGam3"
    ],
    "adapter": {
      "type": "VcfTabixAdapter",
      "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
      "samplesTsvLocation": {
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
      }
    },
    "displays": [
      {
        "type": "LinearMultiSampleVariantDisplay",
        "facet": {
          "field": "karyotype",
          "domain": [
            "2L+a/2L+a",
            "2La/2L+a",
            "2La/2La"
          ]
        },
        "rowColor": "karyotype",
        "referenceDrawingMode": "skip",
        "showLegend": false,
        "height": 170
      }
    ]
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/ucsc/anoGam3/config.json \
  --tracks tracks.json \
  --assembly anoGam3 --loc chr2L \
  --track ag1000g_2l_loci display:LinearBasicDisplay '{"height":40}' \
  --track ag1000g_2l_cmgam display:LDTrackDisplay \
  --track ag1000g_2la_karyotype_cmgam display:LinearMultiSampleVariantDisplay \
  --track ag1000g_2l_gagam display:LDTrackDisplay \
  --track ag1000g_2la_karyotype_gagam display:LinearMultiSampleVariantDisplay \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

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'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ag1000g_2l_loci",
      "name": "2L loci",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "ag1000g_2l_loci",
        "features": [
          {
            "uniqueId": "vgsc",
            "refName": "chr2L",
            "start": 2358158,
            "end": 2431617,
            "name": "Vgsc",
            "type": "gene"
          },
          {
            "uniqueId": "two_la",
            "refName": "chr2L",
            "start": 20524058,
            "end": 42165532,
            "name": "2La",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_cmgam",
      "name": "Cameroon, both arrangements segregating (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_CMgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "variantLayout": "genomic",
          "showLegend": true,
          "squashToHeight": false,
          "height": 340
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_cmgam",
      "name": "Cameroon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_CMgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "facet": {
            "field": "karyotype",
            "domain": [
              "2L+a/2L+a",
              "2La/2L+a",
              "2La/2La"
            ]
          },
          "rowColor": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": true,
          "height": 200
        }
      ]
    },
    {
      "type": "LDTrack",
      "trackId": "ag1000g_2l_gagam",
      "name": "Gabon, one arrangement in almost every mosquito (r²)",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "PlinkLDTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2L_GAgam.ld.gz"
      },
      "displays": [
        {
          "type": "LDTrackDisplay",
          "ldMetric": "r2",
          "variantLayout": "genomic",
          "showLegend": true,
          "squashToHeight": false,
          "height": 250
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "ag1000g_2la_karyotype_gagam",
      "name": "Gabon, one row per mosquito",
      "assemblyNames": [
        "anoGam3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam.vcf.gz",
        "samplesTsvLocation": {
          "uri": "https://jbrowse.org/demos/popgen/ag1000g_2La_GAgam_samples.tsv"
        }
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "facet": {
            "field": "karyotype",
            "domain": [
              "2L+a/2L+a",
              "2La/2L+a",
              "2La/2La"
            ]
          },
          "rowColor": "karyotype",
          "referenceDrawingMode": "skip",
          "showLegend": false,
          "height": 170
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "anoGam3",
      "loc": "chr2L",
      "tracks": [
        {
          "trackId": "ag1000g_2l_loci",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "ag1000g_2l_cmgam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_cmgam",
          "type": "LinearMultiSampleVariantDisplay"
        },
        {
          "trackId": "ag1000g_2l_gagam",
          "type": "LDTrackDisplay"
        },
        {
          "trackId": "ag1000g_2la_karyotype_gagam",
          "type": "LinearMultiSampleVariantDisplay"
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/ucsc/anoGam3/config.json \
  --width 1500 --height 1395 \
  --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.

The domain in each case is a genetics decision, not an alphabetical one: dosage order in the mosquito figure, standard-before-carrier in the fly figure, both read straight off the figure's caption. Population genomics and LD in mosquitoes work through both.

The mark display

LinearMarkDisplay takes the same facet object, and separately, a row channel that packs features within a section (a BAM's own pileup, or any mark whose transform runs a pileup step). Faceting and row-packing are independent — a facet splits into sections first, and each mark packs its own rows inside each section:

HG002 ONT reads faceted by their HP tag: each haplotype's reads packed into a separate band under the chip that names it, and the untagged reads in a third. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

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%22sessionTracks%22%3A%5B%7B%22type%22%3A%22AlignmentsTrack%22%2C%22trackId%22%3A%22snrpn_facet%22%2C%22name%22%3A%22HG002+ONT+reads+faceted+by+HP%22%2C%22assemblyNames%22%3A%5B%22hg38%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BamAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fmethylation%2FHG002_SNRPN_5mC_haplotagged.bam%22%7D%2C%22displays%22%3A%5B%7B%22type%22%3A%22LinearMarkDisplay%22%2C%22displayId%22%3A%22snrpn_facet-LinearMarkDisplay%22%2C%22transform%22%3A%5B%7B%22type%22%3A%22formula%22%2C%22expr%22%3A%22jexl%3AgetTag%28feature%2C%27HP%27%29%22%2C%22as%22%3A%22HP%22%7D%5D%2C%22facet%22%3A%22HP%22%2C%22marks%22%3A%5B%7B%22mark%22%3A%22span%22%2C%22transform%22%3A%5B%7B%22type%22%3A%22pileup%22%7D%5D%2C%22encoding%22%3A%7B%22row%22%3A%22row%22%2C%22color%22%3A%7B%22field%22%3A%22HP%22%2C%22scale%22%3A%22categorical%22%2C%22title%22%3A%22Haplotype%22%7D%7D%7D%5D%7D%5D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr15%3A24%2C900%2C000-25%2C000%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22snrpn_facet%22%2C%22type%22%3A%22LinearMarkDisplay%22%2C%22height%22%3A400%2C%22forceLoad%22%3Atrue%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+mark_display%2Ffacet

With your own data, the steps behind the figure:

  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 BAM file (.bam + .bai).This figure uses “HG002 ONT reads faceted by HP”.
    1. Drag the bar at the bottom edge of the track to resize it (400px here).
    2. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.
  3. Type your region of interest into the location box and press Enter.This figure is at chr15:24,900,000-25,000,000.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.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 BAM file (.bam + .bai).This figure uses “HG002 ONT reads faceted by HP”.
    1. Drag the bar at the bottom edge of the track to resize it (400px here).
    2. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.
  3. Type your region of interest into the location box and press Enter.This figure is at chr15:24,900,000-25,000,000.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "AlignmentsTrack",
  "trackId": "snrpn_facet",
  "name": "HG002 ONT reads faceted by HP",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "BamAdapter",
    "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "displayId": "snrpn_facet-LinearMarkDisplay",
      "transform": [
        {
          "type": "formula",
          "expr": "jexl:getTag(feature,'\''HP'\'')",
          "as": "HP"
        }
      ],
      "facet": "HP",
      "marks": [
        {
          "mark": "span",
          "transform": [
            {
              "type": "pileup"
            }
          ],
          "encoding": {
            "row": "row",
            "color": {
              "field": "HP",
              "scale": "categorical",
              "title": "Haplotype"
            }
          }
        }
      ]
    }
  ]
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs hg38 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure from test_data/config_demo.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "sessionTracks": [
    {
      "type": "AlignmentsTrack",
      "trackId": "snrpn_facet",
      "name": "HG002 ONT reads faceted by HP",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "BamAdapter",
        "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
      },
      "displays": [
        {
          "type": "LinearMarkDisplay",
          "displayId": "snrpn_facet-LinearMarkDisplay",
          "transform": [
            {
              "type": "formula",
              "expr": "jexl:getTag(feature,'HP')",
              "as": "HP"
            }
          ],
          "facet": "HP",
          "marks": [
            {
              "mark": "span",
              "transform": [
                {
                  "type": "pileup"
                }
              ],
              "encoding": {
                "row": "row",
                "color": {
                  "field": "HP",
                  "scale": "categorical",
                  "title": "Haplotype"
                }
              }
            }
          ]
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr15:24,900,000-25,000,000",
      "tracks": [
        {
          "trackId": "snrpn_facet",
          "type": "LinearMarkDisplay",
          "height": 400,
          "forceLoad": true
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/config_demo.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "AlignmentsTrack",
            "trackId": "snrpn_facet",
            "name": "HG002 ONT reads faceted by HP",
            "assemblyNames": [
                "hg38"
            ],
            "adapter": {
                "type": "BamAdapter",
                "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
            },
            "displays": [
                {
                    "type": "LinearMarkDisplay",
                    "displayId": "snrpn_facet-LinearMarkDisplay",
                    "transform": [
                        {
                            "type": "formula",
                            "expr": "jexl:getTag(feature,'HP')",
                            "as": "HP"
                        }
                    ],
                    "facet": "HP",
                    "marks": [
                        {
                            "mark": "span",
                            "transform": [
                                {
                                    "type": "pileup"
                                }
                            ],
                            "encoding": {
                                "row": "row",
                                "color": {
                                    "field": "HP",
                                    "scale": "categorical",
                                    "title": "Haplotype"
                                }
                            }
                        }
                    ]
                }
            ]
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr15:24,900,000-25,000,000",
            "tracks": [
                {
                    "trackId": "snrpn_facet",
                    "type": "LinearMarkDisplay",
                    "height": 400,
                    "forceLoad": True
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

cat > tracks.json <<'JSON'
[
  {
    "type": "AlignmentsTrack",
    "trackId": "snrpn_facet",
    "name": "HG002 ONT reads faceted by HP",
    "assemblyNames": [
      "hg38"
    ],
    "adapter": {
      "type": "BamAdapter",
      "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
    },
    "displays": [
      {
        "type": "LinearMarkDisplay",
        "displayId": "snrpn_facet-LinearMarkDisplay",
        "transform": [
          {
            "type": "formula",
            "expr": "jexl:getTag(feature,'HP')",
            "as": "HP"
          }
        ],
        "facet": "HP",
        "marks": [
          {
            "mark": "span",
            "transform": [
              {
                "type": "pileup"
              }
            ],
            "encoding": {
              "row": "row",
              "color": {
                "field": "HP",
                "scale": "categorical",
                "title": "Haplotype"
              }
            }
          }
        ]
      }
    ]
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --tracks tracks.json \
  --assembly hg38 --loc chr15:24,900,000-25,000,000 \
  --track snrpn_facet display:LinearMarkDisplay '{"height":400,"forceLoad":true}' \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

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'
{
  "sessionTracks": [
    {
      "type": "AlignmentsTrack",
      "trackId": "snrpn_facet",
      "name": "HG002 ONT reads faceted by HP",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "BamAdapter",
        "uri": "https://jbrowse.org/demos/methylation/HG002_SNRPN_5mC_haplotagged.bam"
      },
      "displays": [
        {
          "type": "LinearMarkDisplay",
          "displayId": "snrpn_facet-LinearMarkDisplay",
          "transform": [
            {
              "type": "formula",
              "expr": "jexl:getTag(feature,'HP')",
              "as": "HP"
            }
          ],
          "facet": "HP",
          "marks": [
            {
              "mark": "span",
              "transform": [
                {
                  "type": "pileup"
                }
              ],
              "encoding": {
                "row": "row",
                "color": {
                  "field": "HP",
                  "scale": "categorical",
                  "title": "Haplotype"
                }
              }
            }
          ]
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr15:24,900,000-25,000,000",
      "tracks": [
        {
          "trackId": "snrpn_facet",
          "type": "LinearMarkDisplay",
          "height": 400,
          "forceLoad": true
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --width 1500 --height 610 \
  --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.

The mark display guide's Facets section has the full mechanism, including how the track menu's Sections list writes a drag back into domain.

Multiway synteny

MultiWaySyntenyDisplay draws one lane per assembly rather than one section per field value, so there is no facet — domain sits directly on the display and lists assembly names. It composes with ribbonColor, which paints each ribbon by a field of its own — here, the relative strand between the two lanes a ribbon joins:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_cacao_blocks",
  "name": "Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks)",
  "assemblyNames": [
    "grape",
    "peach",
    "cacao",
    "poplar",
    "citrus",
    "arabidopsis",
    "tomato"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "grape_peach_cacao.blocks",
    "blockAssemblies": [
      "grape",
      "peach",
      "cacao",
      "poplar",
      "citrus",
      "arabidopsis",
      "tomato"
    ],
    "bedLocations": [
      "grape.bed",
      "peach.bed",
      "cacao.bed",
      "poplar.bed",
      "citrus.bed",
      "arabidopsis.bed",
      "tomato.bed"
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "displayId": "grape_peach_cacao_blocks-MultiWaySyntenyDisplay",
      "domain": ["peach", "cacao", "poplar", "citrus", "arabidopsis", "tomato"],
      "ribbonColor": { "field": "strand" }
    }
  ]
}
jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_cacao_blocks",
  "name": "Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks)",
  "assemblyNames": [
    "grape",
    "peach",
    "cacao",
    "poplar",
    "citrus",
    "arabidopsis",
    "tomato"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "grape_peach_cacao.blocks",
    "blockAssemblies": [
      "grape",
      "peach",
      "cacao",
      "poplar",
      "citrus",
      "arabidopsis",
      "tomato"
    ],
    "bedLocations": [
      "grape.bed",
      "peach.bed",
      "cacao.bed",
      "poplar.bed",
      "citrus.bed",
      "arabidopsis.bed",
      "tomato.bed"
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "displayId": "grape_peach_cacao_blocks-MultiWaySyntenyDisplay",
      "domain": ["peach", "cacao", "poplar", "citrus", "arabidopsis", "tomato"],
      "ribbonColor": { "field": "strand" }
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_cacao_blocks",
  "name": "Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks)",
  "assemblyNames": [
    "grape",
    "peach",
    "cacao",
    "poplar",
    "citrus",
    "arabidopsis",
    "tomato"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "grape_peach_cacao.blocks",
    "blockAssemblies": [
      "grape",
      "peach",
      "cacao",
      "poplar",
      "citrus",
      "arabidopsis",
      "tomato"
    ],
    "bedLocations": [
      "grape.bed",
      "peach.bed",
      "cacao.bed",
      "poplar.bed",
      "citrus.bed",
      "arabidopsis.bed",
      "tomato.bed"
    ]
  },
  "displays": [
    {
      "type": "MultiWaySyntenyDisplay",
      "displayId": "grape_peach_cacao_blocks-MultiWaySyntenyDisplay",
      "domain": ["peach", "cacao", "poplar", "citrus", "arabidopsis", "tomato"],
      "ribbonColor": { "field": "strand" }
    }
  ]
}

grape_peach_cacao.blocks, grape.bed, peach.bed, cacao.bed, poplar.bed, citrus.bed, arabidopsis.bed, tomato.bed are relative to a config.json. Replace each with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

The same grape locus over seven genomes, lanes pinned by retention, ribbons colored by relative strand: red where a lane's orientation matches the one above it, blue where it is inverted. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

Nothing happens?

Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fgrape_peach_cacao%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22GCF_030704535.1%22%2C%22loc%22%3A%22chr11%3A778%2C000-866%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_030704535.1-ncbiRefSeq%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%2C%22displayMode%22%3A%22compact%22%2C%22showLabels%22%3A%22auto%22%7D%2C%7B%22trackId%22%3A%22grape_peach_cacao_blocks%22%2C%22type%22%3A%22MultiWaySyntenyDisplay%22%2C%22domain%22%3A%5B%22GCF_000346465.2%22%2C%22GCF_000208745.1%22%2C%22poplar%22%2C%22citrus%22%2C%22arabidopsis%22%2C%22tomato%22%5D%2C%22ribbonColor%22%3A%7B%22field%22%3A%22strand%22%7D%2C%22height%22%3A340%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+multiway_synteny%2Flgv_track_lanes_colored

With your own data, the steps behind the figure:

  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 GCF_030704535.1, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “NCBI RefSeq - RefSeq All”.
    1. Track menu → Show only genes (checked)
    2. Track menu → Feature height → Compact
    3. Track menu → Show... → Labels → Auto
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks)”.
    1. Track menu → Color by... → Ribbons → Strand
    2. Drag the bar at the bottom edge of the track to resize it (340px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr11:778,000-866,000.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses GCF_030704535.1, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “NCBI RefSeq - RefSeq All”.
    1. Track menu → Show only genes (checked)
    2. Track menu → Feature height → Compact
    3. Track menu → Show... → Labels → Auto
  3. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses “Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks)”.
    1. Track menu → Color by... → Ribbons → Strand
    2. Drag the bar at the bottom edge of the track to resize it (340px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr11:778,000-866,000.

Some settings have no written step yet — see the Spec tab.

This session spec draws the figure from https://jbrowse.org/demos/grape_peach_cacao/config.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GCF_030704535.1",
      "loc": "chr11:778,000-866,000",
      "tracks": [
        {
          "trackId": "GCF_030704535.1-ncbiRefSeq",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact",
          "showLabels": "auto"
        },
        {
          "trackId": "grape_peach_cacao_blocks",
          "type": "MultiWaySyntenyDisplay",
          "domain": [
            "GCF_000346465.2",
            "GCF_000208745.1",
            "poplar",
            "citrus",
            "arabidopsis",
            "tomato"
          ],
          "ribbonColor": {
            "field": "strand"
          },
          "height": 340
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "GCF_030704535.1",
            "loc": "chr11:778,000-866,000",
            "tracks": [
                {
                    "trackId": "GCF_030704535.1-ncbiRefSeq",
                    "type": "LinearBasicDisplay",
                    "showOnlyGenes": True,
                    "displayMode": "compact",
                    "showLabels": "auto"
                },
                {
                    "trackId": "grape_peach_cacao_blocks",
                    "type": "MultiWaySyntenyDisplay",
                    "domain": [
                        "GCF_000346465.2",
                        "GCF_000208745.1",
                        "poplar",
                        "citrus",
                        "arabidopsis",
                        "tomato"
                    ],
                    "ribbonColor": {
                        "field": "strand"
                    },
                    "height": 340
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --assembly GCF_030704535.1 --loc chr11:778,000-866,000 \
  --track GCF_030704535.1-ncbiRefSeq display:LinearBasicDisplay '{"showOnlyGenes":true,"displayMode":"compact","showLabels":"auto"}' \
  --track grape_peach_cacao_blocks display:MultiWaySyntenyDisplay '{"domain":["GCF_000346465.2","GCF_000208745.1","poplar","citrus","arabidopsis","tomato"],"ribbonColor":{"field":"strand"},"height":340}' \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

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": "GCF_030704535.1",
      "loc": "chr11:778,000-866,000",
      "tracks": [
        {
          "trackId": "GCF_030704535.1-ncbiRefSeq",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact",
          "showLabels": "auto"
        },
        {
          "trackId": "grape_peach_cacao_blocks",
          "type": "MultiWaySyntenyDisplay",
          "domain": [
            "GCF_000346465.2",
            "GCF_000208745.1",
            "poplar",
            "citrus",
            "arabidopsis",
            "tomato"
          ],
          "ribbonColor": {
            "field": "strand"
          },
          "height": 340
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 680 \
  --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.

Unlisted assemblies still get a lane — they stack below the named ones, densest-first, so a ribbon chain through them is cut as late as possible. The synteny track guide covers the adapter side, and the grape/peach/cacao tutorial works through picking the lane order itself.

Row-partitioned tracks

LinearMultiRowFeatureDisplay fixes one row per value rather than a foldable section — no chip, no hide, no overflow merge — through rows instead of facet, with the same domain. Nine ENCODE cell types, pinned to ENCODE's own tiers rather than alphabetical order:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "broad_chromhmm_multirow_hg19",
  "name": "ChromHMM chromatin state (Broad ENCODE, 9 cell types)",
  "assemblyNames": ["hg19"],
  "category": ["ENCODE", "Chromatin state"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "wgEncodeBroadHmm.multirow.bed.gz"
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "cellType",
        "domain": [
          "GM12878",
          "H1-hESC",
          "K562",
          "HepG2",
          "HUVEC",
          "HMEC",
          "HSMM",
          "NHEK",
          "NHLF"
        ]
      },
      "height": 200
    }
  ]
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "broad_chromhmm_multirow_hg19",
  "name": "ChromHMM chromatin state (Broad ENCODE, 9 cell types)",
  "assemblyNames": ["hg19"],
  "category": ["ENCODE", "Chromatin state"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "wgEncodeBroadHmm.multirow.bed.gz"
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "cellType",
        "domain": [
          "GM12878",
          "H1-hESC",
          "K562",
          "HepG2",
          "HUVEC",
          "HMEC",
          "HSMM",
          "NHEK",
          "NHLF"
        ]
      },
      "height": 200
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "broad_chromhmm_multirow_hg19",
  "name": "ChromHMM chromatin state (Broad ENCODE, 9 cell types)",
  "assemblyNames": ["hg19"],
  "category": ["ENCODE", "Chromatin state"],
  "adapter": {
    "type": "BedTabixAdapter",
    "uri": "wgEncodeBroadHmm.multirow.bed.gz"
  },
  "displays": [
    {
      "type": "LinearMultiRowFeatureDisplay",
      "rows": {
        "field": "cellType",
        "domain": [
          "GM12878",
          "H1-hESC",
          "K562",
          "HepG2",
          "HUVEC",
          "HMEC",
          "HSMM",
          "NHEK",
          "NHLF"
        ]
      },
      "height": 200
    }
  ]
}

wgEncodeBroadHmm.multirow.bed.gz is relative to a config.json. Replace it with its URL or its path on this computer.

The same mechanism at a larger scale — a rows.domain of six names, with rows.kept narrowing a 127-epigenome track to the three tissues a figure is actually about, in the order the comparison reads:

Lung fibroblasts, foreskin fibroblasts and ES cells over HOXA. Lung fibroblasts keep HOXA1-A7 (red box) active and HOXA9-A13 (blue box) Polycomb-repressed, foreskin fibroblasts the reverse, and ES cells hold the whole cluster repressed. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session.

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%22hg19%22%2C%22loc%22%3A%22chr7%3A27%2C110%2C000-27%2C265%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_gff_hg19%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showLabels%22%3A%22name%22%2C%22jexlFiltersSetting%22%3A%5B%22jexl%3Afeature.type%21%3D%27pseudogene%27%22%5D%2C%22height%22%3A110%7D%2C%7B%22trackId%22%3A%22roadmap_chromhmm_multirow_hg19%22%2C%22type%22%3A%22LinearMultiRowFeatureDisplay%22%2C%22rows%22%3A%7B%22field%22%3A%22cellType%22%2C%22domain%22%3A%5B%22NHLF+Lung+Fibroblast+Primary+Cells%22%2C%22IMR90+fetal+lung+fibroblasts+Cell+Line%22%2C%22Foreskin+Fibroblast+Primary+Cells+skin01%22%2C%22Foreskin+Fibroblast+Primary+Cells+skin02%22%2C%22H1+Cells%22%2C%22H9+Cells%22%5D%2C%22kept%22%3A%5B%22NHLF+Lung+Fibroblast+Primary+Cells%22%2C%22IMR90+fetal+lung+fibroblasts+Cell+Line%22%2C%22Foreskin+Fibroblast+Primary+Cells+skin01%22%2C%22Foreskin+Fibroblast+Primary+Cells+skin02%22%2C%22H1+Cells%22%2C%22H9+Cells%22%5D%7D%2C%22rowGroups%22%3A%5B%5D%2C%22height%22%3A240%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+chromhmm_hoxa_fibroblasts

With your own data, the steps behind the figure:

  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 hg19, 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 genes (hg19)”.
    1. Track menu → Show... → Labels → Name only
    2. Track menu → Filter by... → add the expressionThis figure filters on feature.type!='pseudogene'.
    3. Drag the bar at the bottom edge of the track to resize it (110px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “ChromHMM chromatin state (Roadmap, 127 epigenomes)”.
    1. Track menu → Partition by... → cellTypeThe list is built from the attributes the loaded features carry, so a track whose data has not loaded yet offers nothing.
    2. Drag the bar at the bottom edge of the track to resize it (240px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr7:27,110,000-27,265,000.

Some settings have no written step yet — see the Spec tab.

Open this view in JBrowse Web ↗

Its genome and tracks are hosted, so File → Open track... there adds your own files beside them.

With your own data, the steps behind the figure:

  1. Put your genome in your JBrowse Web's config.json: jbrowse add-assembly adds it.This figure uses hg19, 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 genes (hg19)”.
    1. Track menu → Show... → Labels → Name only
    2. Track menu → Filter by... → add the expressionThis figure filters on feature.type!='pseudogene'.
    3. Drag the bar at the bottom edge of the track to resize it (110px here).
  3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “ChromHMM chromatin state (Roadmap, 127 epigenomes)”.
    1. Track menu → Partition by... → cellTypeThe list is built from the attributes the loaded features carry, so a track whose data has not loaded yet offers nothing.
    2. Drag the bar at the bottom edge of the track to resize it (240px here).
  4. Type your region of interest into the location box and press Enter.This figure is at chr7:27,110,000-27,265,000.

Some settings have no written step yet — see the Spec tab.

This session spec draws the figure from test_data/config_demo.json: paste it after &session=spec- on a JBrowse Web link that loads that config.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg19",
      "loc": "chr7:27,110,000-27,265,000",
      "tracks": [
        {
          "trackId": "ncbi_gff_hg19",
          "type": "LinearBasicDisplay",
          "showLabels": "name",
          "jexlFiltersSetting": [
            "jexl:feature.type!='pseudogene'"
          ],
          "height": 110
        },
        {
          "trackId": "roadmap_chromhmm_multirow_hg19",
          "type": "LinearMultiRowFeatureDisplay",
          "rows": {
            "field": "cellType",
            "domain": [
              "NHLF Lung Fibroblast Primary Cells",
              "IMR90 fetal lung fibroblasts Cell Line",
              "Foreskin Fibroblast Primary Cells skin01",
              "Foreskin Fibroblast Primary Cells skin02",
              "H1 Cells",
              "H9 Cells"
            ],
            "kept": [
              "NHLF Lung Fibroblast Primary Cells",
              "IMR90 fetal lung fibroblasts Cell Line",
              "Foreskin Fibroblast Primary Cells skin01",
              "Foreskin Fibroblast Primary Cells skin02",
              "H1 Cells",
              "H9 Cells"
            ]
          },
          "rowGroups": [],
          "height": 240
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/code/jb2/main/test_data/config_demo.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg19",
            "loc": "chr7:27,110,000-27,265,000",
            "tracks": [
                {
                    "trackId": "ncbi_gff_hg19",
                    "type": "LinearBasicDisplay",
                    "showLabels": "name",
                    "jexlFiltersSetting": [
                        "jexl:feature.type!='pseudogene'"
                    ],
                    "height": 110
                },
                {
                    "trackId": "roadmap_chromhmm_multirow_hg19",
                    "type": "LinearMultiRowFeatureDisplay",
                    "rows": {
                        "field": "cellType",
                        "domain": [
                            "NHLF Lung Fibroblast Primary Cells",
                            "IMR90 fetal lung fibroblasts Cell Line",
                            "Foreskin Fibroblast Primary Cells skin01",
                            "Foreskin Fibroblast Primary Cells skin02",
                            "H1 Cells",
                            "H9 Cells"
                        ],
                        "kept": [
                            "NHLF Lung Fibroblast Primary Cells",
                            "IMR90 fetal lung fibroblasts Cell Line",
                            "Foreskin Fibroblast Primary Cells skin01",
                            "Foreskin Fibroblast Primary Cells skin02",
                            "H1 Cells",
                            "H9 Cells"
                        ]
                    },
                    "rowGroups": [],
                    "height": 240
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --assembly hg19 --loc chr7:27,110,000-27,265,000 \
  --track ncbi_gff_hg19 display:LinearBasicDisplay '{"showLabels":"name","jexlFiltersSetting":["jexl:feature.type!='\''pseudogene'\''"],"height":110}' \
  --track roadmap_chromhmm_multirow_hg19 display:LinearMultiRowFeatureDisplay '{"rows":{"field":"cellType","domain":["NHLF Lung Fibroblast Primary Cells","IMR90 fetal lung fibroblasts Cell Line","Foreskin Fibroblast Primary Cells skin01","Foreskin Fibroblast Primary Cells skin02","H1 Cells","H9 Cells"],"kept":["NHLF Lung Fibroblast Primary Cells","IMR90 fetal lung fibroblasts Cell Line","Foreskin Fibroblast Primary Cells skin01","Foreskin Fibroblast Primary Cells skin02","H1 Cells","H9 Cells"]},"rowGroups":[],"height":240}' \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

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": "hg19",
      "loc": "chr7:27,110,000-27,265,000",
      "tracks": [
        {
          "trackId": "ncbi_gff_hg19",
          "type": "LinearBasicDisplay",
          "showLabels": "name",
          "jexlFiltersSetting": [
            "jexl:feature.type!='pseudogene'"
          ],
          "height": 110
        },
        {
          "trackId": "roadmap_chromhmm_multirow_hg19",
          "type": "LinearMultiRowFeatureDisplay",
          "rows": {
            "field": "cellType",
            "domain": [
              "NHLF Lung Fibroblast Primary Cells",
              "IMR90 fetal lung fibroblasts Cell Line",
              "Foreskin Fibroblast Primary Cells skin01",
              "Foreskin Fibroblast Primary Cells skin02",
              "H1 Cells",
              "H9 Cells"
            ],
            "kept": [
              "NHLF Lung Fibroblast Primary Cells",
              "IMR90 fetal lung fibroblasts Cell Line",
              "Foreskin Fibroblast Primary Cells skin01",
              "Foreskin Fibroblast Primary Cells skin02",
              "H1 Cells",
              "H9 Cells"
            ]
          },
          "rowGroups": [],
          "height": 240
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/config_demo.json \
  --width 1500 --height 620 \
  --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.

The ChromHMM tutorial has both tracks in full, plus what an unset rows.domain does instead: Cluster rows by similarity... derives a row order from the data itself.

Reordering at runtime

Every one of these displays writes a drag-to-reorder back into the same domain slot it read the curated order from — the gene track and mark display's Sections list, the alignments track menu's group-by sections, multiway synteny's Lanes menu and lane-header drag, and the multi-row display's row drag, which writes rows.domain. A session saved after reordering carries the new order in config.json terms, not as separate runtime-only state.

See also