Cbioportal: More compact OncoPrint tab

[schultzn]

I propose to slightly redesign the OncoPrint tab. Two options below. Thoughts?

Option 2 is probably better, as the case list and alteration frequency is already shown above the tab.

But if we go with option 2, where would information about multiple samples per patient go?

[schultzn]

Adding option 3

[jjgao]

I like option two better too. We have the the show patient/sample option under View menu -- would that be sufficient?

[schultzn]

I think that is too hidden.

On Oct 9, 2018, at 22:01, JianJiong Gao [e-mail] wrote:

I like option two better too. We have the the show patient/sample option under View menu -- would that be sufficient?

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[schultzn]

I think we should find a way to indicate to the user when multiple samples from a single patient were merged.

On Oct 9, 2018, at 22:45, Nikolaus Schultz [e-mail] wrote:

I think that is too hidden.

On Oct 9, 2018, at 22:01, JianJiong Gao [e-mail] wrote:

I like option two better too. We have the the show patient/sample option under View menu -- would that be sufficient?

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[jjgao]

@schultzn maybe we can have a clinical track to indicate the number of samples per patient when multiple samples from a single patient were merged? We can then have a submenu of that track to expand to samples?

[adamabeshouse]

@jjgao @schultzn what about adding this information to the portal header?

[adamabeshouse]

if people need to know specifically which patients have more than one sample, then a clinical track would make sense, but otherwise it seems overly complicated if all they need to know is that some columns contain more than one sample.

[jjgao]

To summarize:

• [x] option 2
  
• [x] add number of patients into header
  
• [x] modify the the header "Gene Set / Pathway is altered in ..." to "Queried gene(s) is/are altered in ..." (switch based on 1 gene or multiple genes)
• [x] add "# samples" clinical attribute track and allow expanding to samples in the track menu
• [x] talis comment

ok, @schultzn?

[schultzn]

I like it! OK!

[tmazor]

I'm a little late to this one but I like this plan also!

However, I think we're going to be missing one thing. The % altered in the header is always at the sample level:

But the % altered in the Oncoprint can be % samples or % patients depending on what is being viewed:

vs

Perhaps we add that to the header? Maybe something like: "Queried gene(s) is/are altered in X (Y%) of queried samples and Z (W%) of queried patients"

[jjgao]

@tmazor good point.

When there is just one sample for every patient, we can do: "Queried gene(s) is/are altered in X (Y%) of queried samples/samples"

[adamabeshouse]

do we want the num samples track to start at 0 or the minimum?

this is starting at 0 (in other words, most have 1)

sorted

this is starting at the data minimum, so that its blank space if at 1

sorted

[jjgao]

@adamabeshouse I think starting at 0 makes sense.

[jjgao]

@schultzn we are now always showing the oncoprint menu as it's not so neat or useful to hide it and leave a blank space. Please comment if you'd like to hide it.

[schultzn]

Yes, looks good.

On Nov 27, 2018, at 10:14 PM, JianJiong Gao [e-mail] wrote:

@schultzn https://github.com/schultzn we are now always showing the oncoprint menu as it's not so neat or useful to hide it and leave a blank space. Please comment if you'd like to hide it.

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