label regions on top of heatmap

[Bo-UT]

Hi,

Is there anyway to label regions on top of the heatmap like jucebox?

I have following region data,
chr10 74160000 74720000 chr10 74165000 74725000
chr12 120920000 121640000 chr12 120925000 121645000
chr15 86360000 88840000 chr15 86365000 88845000

and did clodius,
clodius aggregate bedpe
--assembly hg19
--chr1-col 1 --from1-col 2 --to1-col 3
--chr2-col 4 --from2-col 5 --to2-col 6
--output-file domains.txt.multires
domains.txt

then ingested it.
higlass-manage ingest domains.txt.multires
--filetype bed2ddb
--datatype 2d-rectangle-domains

But I cannot find the ingested domains.txt.multires in http://localhost:8989/app. Any thoughts on it?
Thank you!

Bo

[pkerpedjiev]

Huh... I followed exactly what you did by pasting your data and commands and was able to load the domains.txt file.

Did you get any errors in the higlass-manage ingest command?

Did you try to add it as a track after ingesting?

[xl5525]

Huh... I followed exactly what you did by pasting your data and commands and was able to load the domains.txt file.

Did you get any errors in the higlass-manage ingest command?

Did you try to add it as a track after ingesting?

Hi,

Is there anyway to overlay this "2d-rectangle-domains" with contact maps in the same track?

I found this, but I am not sure whether it can be used for bedpe "2d-rectangle-domains" and where to insert it in the view config.

{
  views: [
    {
      overlays: [
        {
          uid: 'overlay-annotation',
          includes: ['track1Uid', 'track2Uid', 'track3Uid'],
          // Default definitions for annotations
          options: {
            extent: [
              [1000000000, 1100000000],
              [1200000000, 1300000000, 1400000, 1500000]
            ],
            minWidth: 3,
            fill: 'blue',
            fillOpacity: 0.3,
            stroke: 'yellow',
            strokeOpacity: 0.6,
            strokeWidth: 2,
            strokePos: ['left', 'right'],
            outline: 'cyan',
            outlineOpacity: 0.1337,
            outlineWidth: 1.337,
            outlinePos: 'top'
          }
        },
        {
          uid: 'overlay-chromosome-grid',
          includes: ['track1', 'track2', 'track3'],
          type: 'chromosome-grid',
          // Same definitions as the chromosome-grid track
          chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv',
          options: {
            lineStrokeWidth: 1,
            lineStrokeColor: 'grey'
          }
        }
      ]
    }
  ],
}

Thank you!