option to add gaps between different groups based on clinical attribute

[jjgao]

I found people like to add a space between different groups when sorting by a clinical attribute. Maybe we can implement that?

[adamabeshouse]

this wouldn't be too hard to implement. what would be a good UI for this?

[jjgao]

Maybe add another checkbox under View: Show whitespace between sorted clinical groups?

[adamabeshouse]

That's a good idea, so if it's not sorted then there's no effect. That sounds good to me.

[jjgao]

yes.

[adamabeshouse]

let's leave this until after 1.11?

[schultzn]

Love the idea!

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On Nov 10, 2017, at 19:06, Adam Abeshouse ***@***.***> wrote: let's leave this until after 1.11? — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.

[jjgao]

@adamabeshouse yes, we can do this later.

[adamabeshouse]

one question is what if you are sorting by more than one clinical attribute? would it only be the topmost track? or maybe the bottommost? also im assuming this would only be for categorical data?

[jjgao]

Good question. Maybe the bottommost (which basically means all sorted tracks, right?) and see how it looks like?

Yes, only for categorical data.

[adamabeshouse]

I think the utility could depend...

Topmost makes sense to me because that most cleanly defines categories. The sort order is determined top to bottom, so if you have it as the bottommost sorted track then the categories will be split up more, which doesnt seem to be the main thrust of this feature.

Although now I'm noticing in the screenshot that it splits on the bottom track as well, but it doesnt split the bottom "clinical" track. So that could be good too - split on all clinical tracks but dont split up the clinical tracks, only the genetic and heatmap.

[adamabeshouse]

maybe the best way to do this would be as an option in the clinical track menus? to toggle splitting for a particular track. that way there is no confusion about track order

[jjgao]

@adamabeshouse great idea!

[adamabeshouse]

@jjgao @schultzn do we still want to do this?

[schultzn]

Yes, it would be great.

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On Nov 25, 2019, at 17:29, Adam Abeshouse ***@***.***> wrote:  @jjgao @schultzn do we still want to do this? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[adamabeshouse]

@schultzn @jjgao

I have a preliminary implementation:

a few questions now..

1. are the gaps big enough?
2. how do you think the gaps should react with the zoom? should they zoom or stay the same size?
3. should I disable the option when the track is not sorted, or just change the text to say "show gaps when sorted"? or any other text?
4. should it be possible to show gaps based on more than one track?

[schultzn]

Looks great!
1 - yes, gaps look big enough
2 - they should probably stay the same size when zooming
3 - when grouping by the track, maybe automatically sort?
4 - a single track is probably enough

[inodb]

Hey this is really cool! I was wondering, maybe a separate issue. Would it make sense to add oncoprint to the group comparison page? Then each group could be separated by these gaps

[adamabeshouse]

do we want the gaps to be reflected in the mini map? @schultzn @jjgao

[jjgao]

do we want the gaps to be reflected in the mini map?

Sorry this question fell between the cracks. I don't think it's very important so I whichever is easy from an implementation perspective.