Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Group Comparison Lollipop Improvements #9901

Closed
11 tasks done
inodb opened this issue Nov 18, 2022 · 2 comments
Closed
11 tasks done

Group Comparison Lollipop Improvements #9901

inodb opened this issue Nov 18, 2022 · 2 comments
Assignees

Comments

@inodb
Copy link
Member

inodb commented Nov 18, 2022

High priority

  • Show which %/# is currently selected (put this state in URL)
    Screen Shot 2022-11-18 at 11 31 35 AM
  • Selected gene should be in URL
  • Percentage is incorrect (divide per group). E.g. in this GRM3 example. Should be 1 mutation / 26 total samples in group B (3.8% instead of 8.4% as it is now). Also good to mention in the tooltip we are showing # of samples rather than # of patients e.g. 3.8% mutation rate (1/26 samples)

Others:

  • Show Driver vs VUS icons like on results view
    • For the driver annotation source selector let's place it at the top somewhere close to the gene selector, so it is clear it stays enabled when selecting different genes
    Screen Shot 2022-11-18 at 11 33 56 AM
  • Show counts separately for each group
  • Figure out gene selector (show either on same line as highest frequencies or show top frequencies in dropdown)
  • Highest frequency should show only "Mutations" highest frequency (rather than Mut+SV+CNA)
  • Don't show genes without mutations in dropdown (if possible we can potentially sort the dropdown by frequency (i guess we should have these numbers from genomics alterations tab filtered by mutations only)
  • Show absolute counts of mutations into tooltip even when in frequency mode
  • When hovering over a lollipop which exists in both groups, show both tooltips at once

image

@tmazor
Copy link
Contributor

tmazor commented Nov 19, 2022

This is such a great feature to have! Nice work!

I agree with all the comments above, and have some additional comments:

  1. y-axis labels are overlapping in multiple ways:
    image
    https://www.cbioportal.org/comparison/mutations?comparisonId=6138b02de6ebe01a6ee2de0b&featureFlags=group_comparison_mutations_lollipop_plot&unselectedGroups=%5B%22NA%22%2C%22LGG_IDHwt%22%5D

  2. Everywhere else in group comparison we refer to groups with (A) xxxxx and (B) yyyyy, and almost always with consistent coloring also
    image
    image
    At a minimum, I think the (A), (B), etc need to be added to the y-axis labels to help with quickly understanding which group is which (group names can be long and very similar to each other, making it hard to quickly grasp). If there's a way to bring in the color too, that'd be even better.

  3. On the Mutations tab, if I add annotation tracks (eg OncoKB, Hotspots), those tracks remain visible as I switch between genes. It would be great to have that behavior here also.

  4. It would be nice if the tooltip could show both # and %, regardless of the current settings for the y-axis
    image

@inodb
Copy link
Member Author

inodb commented Jan 23, 2023

i think all these are solved. Looks like there is a separate issue for the "only" logic
#9968

@inodb inodb closed this as completed Jan 23, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants