Cbioportal: quick links in Plots tab

[jjgao]

The following is a list of quick links. Each link should be included ONLY if the data types are available for the current query. This can be determined by looking at data source which feeds the data type dropdown of the plots tab. (both axis have the same list)

• IF copy-number & mRNA → expression vs copy-number box plot [mRNA vs CNA]
  
  
  
  • http://bit.ly/2VmWmkI
  
  
• IF methylation & mRNA → expression vs methylation scatter plot [mRNA vs methyl.]
  
  
  
  • http://bit.ly/2VmWmkI
  
  
• IF available → Mutation count vs FGA [Mut# vs FGA]
  
  
  
  • http://bit.ly/2VmWmkI
  
  
• IF cancer type detailed >1 and <=15 → Mutation count vs cancer type detailed [Mut# vs Dx]
  
  
  
  • http://bit.ly/2VmWmkI
  
  
• ELSIF cancer type detailed >15 → Mutation count vs cancer type [Mut# vs Dx]
  
  
  
  • http://bit.ly/2M8kc0I
  
  
• IF mRNA & cancer type detailed >1 → mRNA vs cancer type detailed [mRNA vs Dx]
  
  
  
  • http://bit.ly/2VmWmkI
  
  
• IF mRNA and mutation count > 0 → mRNA vs mutation type [mRNA vs mut type]
  
  
  
  • http://bit.ly/2VmWmkI
  
  
• IF mRNA & protein → mRNA vs protein scatter plot [Protein vs mRNA]
  
  
  
  • http://bit.ly/2Oj1h62 (only mass spec is working now)
  
  
• IF treatments → sample order vs treatment IC50 [Tx Waterfall]
  
  
  
  • http://bit.ly/2AEh6fD
  
  

@jjgao @schultzn @adamabeshouse, would it make sense to put the plot tab parameters in the url so it's linkeable? it would actually be a bit complicated to do so because it could become stale easily, but i'm just wondering if it would be desirable?

[jjgao]

Notifying @tmazor @schultzn @cBioPortal/product

[Sjoerd-van-Hagen]

I like the idea of having examples. My main concern is how we will implement this in a way that does not clutter up the interface, which already has a considerable number of bells and whistles.

[schultzn]

Here is a suggestion

[alisman]

@schultzn i think that works. i do think they need a label ("Quick links?"). We have Quick Filters in study page. Perhaps we can reuse the white bar under the nav. @Luke-Sikina this can be your ticket. i will work on making a more descriptive spec.

[schultzn]

So something like this?

[alisman]

exactly. i don't think it essential, but nice to follow convention. they're also centered on study page. could go either way on this. and we don't have to decide now to start implementation.

[adamabeshouse]

@jjgao I think putting it in the URL would be definitely doable and wouldn't go stale so easily - we can use the data type enum, profile id, and gene id? the issue I think would be the URL would get really long..

[jjgao]

@adamabeshouse @alisman we should look into options for storing states in url and in session service. Maybe it's time to work it out? https://github.com/cBioPortal/cbioportal/issues/5525

Maybe for this ticket here, we don't have to worry about it as long as the users can click and get to the plots? Or is it a good opportunity to make saving state happen?

[adamabeshouse]

@jjgao @alisman my sense is lets just focus on the feature, I think. saving state is more in depth and I think will take a while to shake out. thoughts?

[jjgao]

@adamabeshouse that sounds good to me.

[Luke-Sikina]

Just starting this issue. Here's my summary after reading through this.

• create all valid quick links, as described in the main issue
• style the quick links similar to the study page, but also refer to the mock
• don't bother with the url for now, feature has value without it and there seems to be ongoing discussion about if / how

Please let me know if I missed anything.

[Sjoerd-van-Hagen]

So something like this?

Looks good but I would change 'Quick links' to 'Examples' or 'Example plots'.

[alisman]

👍

On Fri, Oct 4, 2019 at 3:06 AM Sjoerd-van-Hagen [e-mail]
wrote:

So something like this?

Looks good but I would change 'Quick links' to 'Examples' or 'Example
plots'.

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[tmazor]

@Luke-Sikina can we try this order?

IF cancer type detailed >1 and <=15 → Mutation count vs cancer type detailed [Mut# vs Dx]
ELSIF cancer type detailed >15 → Mutation count vs cancer type [Mut# vs Dx]
IF available → Mutation count vs FGA [Mut# vs FGA]
IF mRNA & cancer type detailed >1 → mRNA vs cancer type detailed [mRNA vs Dx]
IF mRNA and mutation count > 0 → mRNA vs mutation type [mRNA vs mut type]
IF copy-number & mRNA → expression vs copy-number box plot [mRNA vs CNA]
IF methylation & mRNA → expression vs methylation scatter plot [mRNA vs methyl]
IF mRNA & protein → mRNA vs protein scatter plot [Protein vs mRNA]
IF treatments → sample order vs treatment IC50 [Tx Waterfall]

[schultzn]

And maybe add FGA vs Cancer Type, so:

IF cancer type detailed >1 and <=15 → Mutation count vs cancer type detailed [Mut# vs Dx]
ELSIF cancer type detailed >15 → Mutation count vs cancer type [Mut# vs Dx]
IF cancer type detailed >1 and <=15 → FGA vs cancer type detailed [FGA vs Dx]
ELSIF cancer type detailed >15 → FGA vs cancer type [FGA vs Dx]
IF available → Mutation count vs FGA [Mut# vs FGA]
IF mRNA & cancer type detailed >1 → mRNA vs cancer type detailed [mRNA vs Dx]
IF mRNA and mutation count > 0 → mRNA vs mutation type [mRNA vs mut type]
IF copy-number & mRNA → expression vs copy-number box plot [mRNA vs CNA]
IF methylation & mRNA → expression vs methylation scatter plot [mRNA vs methyl]
IF mRNA & protein → mRNA vs protein scatter plot [Protein vs mRNA]
IF treatments → sample order vs treatment IC50 [Tx Waterfall]