Cbioportal: Hide NA bar in the bar charts of study view

[zhx828]

currently:

Proposed:

https://www.cbioportal.org/study/summary?id=all_phase2_target_2018_pub

[jjgao]

@zhx828 good point. I am wondering if it's possible to use a different shade?

[zhx828]

@jjgao we could, but in a histogram that NA has few samples, the shade does not help much. And they are very easy to be selected.

[jjgao]

Maybe show NA bar as gray similar to pie chart and also allow hiding NA https://github.com/cBioPortal/cbioportal/issues/5204

[jjgao]

@cBioPortal/product thoughts?

[schultzn]

I would not show a bar for NA at all - we could add a number next to the chart, e.g. "NA: 27"

Or is there a good reason to show them in a bar?

[jjgao]

Adding a number instead of a bar is a good idea! Then we don't need to the option to hide NA...

Where should we add "NA: 27"?

[zhx828]

Niki suggested on the top right correct showing NA:27. I will need to generate some mockups to see whether it's feasible.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[jjgao]

@jtquach1 maybe you can help with this?

[jtquach1]

Should a tooltip also display over the NA text when hovered, similar to hovering over the barchart bars?

This is what the chart looks like without the NA bar:

[alisman]

@jtquach1 @cBioPortal/product i think it should be "n/a". there's a little risk the last bar will poke up into it but i guess that's ok.

[Sjoerd-van-Hagen]

Wait, if we remove the NA bar, how do we select samples that are NA?

[jtquach1]

Wait, if we remove the NA bar, how do we select samples that are NA?

I removed the NA from the rendering of the barchart, but didn't touch the NA bar anywhere else; here is a preview of the PR: https://deploy-preview-3497--cbioportalfrontend.netlify.app/study/summary?id=all_phase2_target_2018_pub

[Sjoerd-van-Hagen]

But the user could select samples/patients that have NA for an attribute by
selecting that bar in the bar chart. Now that the NA is not part of the bar
chart anymore, how do I select all samples/patients that have an NA for an
attribute?

--

E. [email protected]

T. [phone]

W. www.thehyve.nl

On Wed, Nov 11, 2020 at 10:34 PM Joyce Quach [e-mail]
wrote:

Wait, if we remove the NA bar, how do we select samples that are NA?

The NA bar is removed from the barchart, but isn't touched anywhere else;
here is a preview of the PR:
https://deploy-preview-3497--cbioportalfrontend.netlify.app/study/summary?id=all_phase2_target_2018_pub

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[jtquach1]

I'd like to clarify: is this by dragging over the barchart bar?

[Sjoerd-van-Hagen]

Yes, indeed.

--

E. [email protected]

T. [phone]

W. www.thehyve.nl

On Wed, Nov 11, 2020 at 10:47 PM Joyce Quach [e-mail]
wrote:

I'd like to clarify: is this by dragging over the barchart bar?
[image: drag_over_na_bar]
https://user-images.githubusercontent.com/33106214/98868016-7fc2a600-243d-11eb-9566-a34677c4a7b8.gif

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[jtquach1]

Yes, indeed.
…
-- E. [email protected] T. [phone] W. www.thehyve.nl
On Wed, Nov 11, 2020 at 10:47 PM Joyce Quach @.*> wrote: I'd like to clarify: is this by dragging over the barchart bar? [image: drag_over_na_bar] https://user-images.githubusercontent.com/33106214/98868016-7fc2a600-243d-11eb-9566-a34677c4a7b8.gif — You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub <#7527 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMGKNN2QXGVIY3XO24SWXDSPMA5ZANCNFSM4NG6JFLQ .

Thank you for the heads up, I'll look into enabling selecting NA samples/patients via clicking on the NA text

[jjgao]

@Sjoerd-van-Hagen good point.

Should we just add a checkbox before n/a for selection? The UI would look ugly, though. In fact, I think it doesn't look great even without the checkbox. One option to make it look better is to only display the n/a text when hovering over the chart. Thoughts? @cBioPortal/product @alisman @zhx828 @inodb

[alisman]

What about just giving the bar a different color and also putting the n/a in the bar to make sure people get it.

Alternately, if it's edge case that people really want to select N/A, then we could prompt user with a dialog when they make selection wit NA? More complicated but ...

[schultzn]

That helps (as would moving it to the side a little). But giving users the option to hide it is also useful, since that could rescale the x-axis, which is useful when there are lots of NAs.

On Nov 12, 2020, at 5:08 PM, alisman [e-mail] wrote:

What about just giving the bar a different color and also putting the n/a in the bar to make sure people get it.

https://user-images.githubusercontent.com/186521/99001874-93d3d980-2509-11eb-8925-3beafc075075.png
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[Sjoerd-van-Hagen]

I prefer the NA to have their own bar indeed, just for uniformity. Giving
it a different color to make it easily distinguished is a good idea. Moving
it away from the other bars would also work.

--

E. [email protected]

T. [phone]

W. www.thehyve.nl

On Thu, Nov 12, 2020 at 11:08 PM alisman [e-mail] wrote:

What about just giving the bar a different color and also putting the n/a
in the bar to make sure people get it.

[image: image]
https://user-images.githubusercontent.com/186521/99001874-93d3d980-2509-11eb-8925-3beafc075075.png

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[Sjoerd-van-Hagen]

But that could also occur when you have a lot of samples which have the
same numeric value...

--

E. [email protected]

T. [phone]

W. www.thehyve.nl

On Thu, Nov 12, 2020 at 11:11 PM schultzn [e-mail] wrote:

That helps (as would moving it to the side a little). But giving users the
option to hide it is also useful, since that could rescale the x-axis,
which is useful when there are lots of NAs.

On Nov 12, 2020, at 5:08 PM, alisman [e-mail] wrote:

What about just giving the bar a different color and also putting the
n/a in the bar to make sure people get it.

<
https://user-images.githubusercontent.com/186521/99001874-93d3d980-2509-11eb-8925-3beafc075075.png

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[jjgao]

giving the bar a different color

+1

giving users the option to hide it is also useful

+1

[Luke-Sikina]

Here's the solution we're going for: Add a check box in the hamburger menu to hide the N/A bar. The bar will be shown by default. The user's decision to hide n/a for each respective chart should be stored in user settings.