Support merged tracks in track hubs

[boehmv]

Dear IGV team,

as a long-term and daily IGV user I am very grateful for your developed tools such as the igv-webapp, which we recently adopted for a project and now heavily use for internal display of our RNA-seq data.

For simplicity, we normally work with .tdf files and merge replicates for individual conditions. Until igv-web version 2.2.7 the track selection was very simple and worked great also with merged .tdf tracks. I wanted to update to igv-web 2.3.5 and use the new tracks selection options (especially the custom-data-modal), but encountered some issues, for which your help would be appreciatedl:

1. The new simple track selection with tickboxes works in principle with merged .tdf files (type: merged), but the already displayed merged tracks are not captured in the tickboxes. In other words, once I tick and load them, close the track selection and open it up again, the already loaded tracks stay not ticked and I could load them again, leading to duplicated display of tracks.
2. I could not get the custom-data-modal track selection to work with merged tracks, since I am not sure how to format the columns such that igv-web would accept the list of tracks. Is there an easy way how I could achieve this goal?
3. Alternatively, is it possible to configure a simple track selection with multiple collapsable "accordion"-like entries, such as the dbVar Hub for hg38 genomes? For normal tracks there is just the "Annotations" header and all tracks listed, but I would like to separate some of them by new collapsable headers.
4. Maybe a naive question, but is it possible to bring back the "old" track selection (e.g. as "type": "simple-data-modal"), since its simplicity would be useful in some situations.

I have to admit that I am not a javascript expert so I apologize if some questions appear basic. Here is a very simple track.json that I used:

{
"label": "2018 RNA-Seq",
"description": "siRNA-KD data",
"tracks": [
{
"name": "(2018) HEK293 control",
"height": 35,
"alpha": 0.75,
"type": "merged",
"order": 7701,
"autoscale": true,
"tracks": [
{
"url": "../data/2018_10/K002000269_94802.tdf",
"color": "#9E9E9E",
"autoscaleGroup": "2018_10"
},
{
"url": "../data/2018_10/K002000269_94804.tdf",
"color": "#9E9E9E",
"autoscaleGroup": "2018_10"
},
{
"url": "../data/2018_10/K002000269_94806.tdf",
"color": "#9E9E9E",
"autoscaleGroup": "2018_10"
}
]
}
]
}

Thanks again and best wishes,
Volker

[jrobinso]

Hi, it will take some time to look into this but just quickly, the "old" track selection should still work, nothing was removed. Do you have a menu configuration that worked previously but does not now?

What's new is track hubs are now supported for menus (in addition to the data modal style).

[boehmv]

Hi Jim, thanks for the quick reply and for looking into these issues.

I have attached a typical json N_AID_UPF1_HCT116.json - which looked like this in version 2.2.7:

and like this in 2.3.5:

I have not changed the file itself and in both cases it is loaded via the trackRegistry.

[jrobinso]

Oh got it. That's just a different presentation style, but it should not be a breaking change. I'll look into it.

[jrobinso]

The "accordion" style load widgets are backed by track hubs. The format can be complex, and is documented at the UCSC browser site, but for simple groupings see "hub.txt" and "groups.txt" here: https://github.com/igvteam/igv-data/tree/main/genomes/hubs/hg19

The "hub.txt" file is then referenced instead of json in the trackRegistry.json file.

[jrobinso]

I've fixed problem (1). Issues (2) and (3) are more difficult, there isn't a representation of merged tracks that work with the data modals, and for now we don't have a 1-1 corresponence with a merged track and UCSC track hub representations. UCSC has merged and overlaid tracks, sot it possible in principle we could do a mapping to an IGV merged track, but at the moment we don't have it. If that's something that would interest you I suggest opening a new ticket, or just rename this one and keep it open. The ticket would be something like "Support merged tracks in track hubs".

[boehmv]

Great, thank you for the fix and the explanation of the other issues.
I will keep this issue open and rename it as you suggested.

Concerning issue (4), do you see an option to enable the "old" Track Selection presentation style - if possible? Thanks!

[jrobinso]

What "old style" are you referring to?

[boehmv]

Basically this one mentioned above (and quoted below). I found the simple list in some cases easier to work with than the individual tickboxes. Maybe I have just missed the option or could not figure out how to bring back the simple list selection.

Hi Jim, thanks for the quick reply and for looking into these issues.

I have attached a typical json N_AID_UPF1_HCT116.json - which looked like this in version 2.2.7:

and like this in 2.3.5:

I have not changed the file itself and in both cases it is loaded via the trackRegistry.

[jrobinso]

Well possibly, but its not a trivial thing as the code has been redesigned for track hubs. The new style dialog supports both the old json and track hubs. But I'll look into it.

[jrobinso]

I think all the issues here are addressed in release 2.4.1 (latest). The json track descriptions will bring up a list-style selection dialog by default. To use the collapsible-section hub style dialogs add "type=hub". I also extended the json syntax to optionally include groups. See https://github.com/igvteam/igv-webapp/blob/master/resources/tracks/mm10_sample.json for an example.