Co-expression: should we overlap with mutaiton data or CNAs?

[jjgao]

Currently, we are overlaying mutational data on top. I couldn't recall why we did that. Would it make more sense to overlay copy number data since CN may have a greater impact on expression?

[adamabeshouse]

One option would be to do both: have checkboxes for Show Mutations and Show CNA, and if both are checked then color if either mutated or CNA, ie "KRAS altered, IPO8 altered, both altered, neither altered"

[tmazor]

Funny you should bring this up - I had a similar thought earlier today when looking at this page. I think we should have options for both. I had been thinking of a toggle like we have on the plots tab, but checkboxes like @adamabeshouse suggested would be even better. Or even better, we could also have an option to define a sample as altered according to the OQL used in the query.

[schultzn]

Agree.. both would be good.. copy-number, makes a lot of sense (and I often wondered why we don’t have it), but we should keep mutations.

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On Mar 20, 2018, at 6:06 PM, Tali Mazor ***@***.***> wrote: Funny you should bring this up - I had a similar thought earlier today when looking at this page. I think we should have options for both. I had been thinking of a toggle like we have on the plots tab, but checkboxes like @adamabeshouse <https://github.com/adamabeshouse> suggested would be even better. Or even better, we could also have an option to define a sample as altered according to the OQL used in the query. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <https://github.com/cBioPortal/cbioportal/issues/4006#issuecomment-374773535>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALV34P4IS3Qx_e7yt-c6Lv6dEa953MGwks5tgX17gaJpZM4Syjkh>.

[jjgao]

For copy number, should we just use "altered or not"? Or differentiate between -2 and 2? What about -1 and 1?

[adamabeshouse]

@jjgao also what to consider altered if both mutation and CNA selected?

[schultzn]

I feel like we used to have this functionality in an old version of the Plots tab? We could try to versions: 1 - Change the outline of each circle to indicate the copy-number change (red, pink, grey, light blue, dark blue) and fill in the circle as we do now to indicate mutation status 2 - Flip the above around and use the circle color for copy-number, and color the outline of the circle differently to indicate mutations. What do people think?

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On Mar 21, 2018, at 1:59 PM, Adam Abeshouse ***@***.***> wrote: @jjgao <https://github.com/jjgao> also what to consider altered if both mutation and CNA selected? — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <https://github.com/cBioPortal/cbioportal/issues/4006#issuecomment-375039630>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALV34LCZO2o7--jS1v090LCT0FEyOciaks5tgpUFgaJpZM4Syjkh>.

[adamabeshouse]

@schultzn as-is I don't think the border will be visible enough for that, but maybe if we thickened it

another option is to use different shapes for mutation status, color for CNA. that may not be very easy to see though..

[schultzn]

Probably.. can you play around with it a bit?

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On Mar 21, 2018, at 5:40 PM, Adam Abeshouse ***@***.***> wrote: @schultzn <https://github.com/schultzn> as-is I don't think the border will be visible enough for that, but maybe if we thickened it — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/cBioPortal/cbioportal/issues/4006#issuecomment-375105229>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALV34OXK0gJZ253WaY9DSE7512AO7lx9ks5tgsjagaJpZM4Syjkh>.

[adamabeshouse]

yes, I will post screenshots

[adamabeshouse]

it just occurred to me this only works in plots tab when the gene is the same, because otherwise which CNA do you show? in plots tab we only show CNA when the gene is the same.

[adamabeshouse]

@schultzn and I discussed and we're going to put this off