Mutations table improvements

[leexgh]

Related tickets and mockup

• Improve annotation column: https://github.com/cBioPortal/cbioportal/issues/8522
• Grouped columns in mutations table: https://github.com/cBioPortal/icebox/issues/189
• Store user settings on what columns are shown for patient view and mutations tab separately: https://github.com/cBioPortal/cbioportal/issues/8521
• Add tooltip for the annotation column in the mutations table: https://github.com/cBioPortal/cbioportal/issues/8305
• Settings for multiple vs single OncoKB icon in annotation column: https://github.com/cBioPortal/cbioportal/issues/8710
• Add Clinical Attributes to Mutations Column Menu: https://github.com/cBioPortal/cbioportal/issues/8657
• Add column-based filters for mutation table (results view) https://github.com/cBioPortal/cbioportal/issues/8713
• Add link to filtered study view in results view mutation table https://github.com/cBioPortal/cbioportal/issues/8802
• OncoKB - cBioPortal integration icon mockups: https://github.com/oncokb/oncokb/issues/2580
• Support grouped columns in LazyMobxTable: https://github.com/cBioPortal/icebox/issues/192
• Mockup: https://docs.google.com/presentation/d/1WNfDmI8cC8cMZ4t8JsFEB2mqR7GmGp2tOY9W0mzAuv4/edit#slide=id.ge0bff99d85_3_288

Improvements

1. Annotation column

1.1 Annotation column header

• Goal:
• Ticket: Add tooltip for the annotation column in the mutations table https://github.com/cBioPortal/cbioportal/issues/8305
• Todo list:
  • [x] Add header and tooltips
  • [x] Leave white space for multiple OncoKB icons
• Status: ready to merge
• Discussion result: Based on the discussion, for now we only support multiple oncokb icons(leave white space between oncokb and civic)
• Assignees: Xiang

1.2 Settings for multiple or single oncokb icons

• Ticket: Settings for multiple vs single OncoKB icon in annotation column https://github.com/cBioPortal/cbioportal/issues/8710
• Discussion result: this will be part of grouped mutation columns(2.4). Once we have the grouped mutation columns, we could either add settings somewhere inside columns menu, or we could have separate columns for single icon oncokb or multiple icons, and we could choose show or hide by adding columns.

1.3 Settings for show or hide annotation sources (superseded by 2.4)

• Ticket: no (mockup slides 14)
• Discussion result: this will be part of grouped mutation columns(2.4). Once we have the grouped mutation columns, we could add settings somewhere inside columns menu along with oncokb single vs multiple icon setting.

1.4 Integration oncokb icon

• Ticket: cBioPortal integration icon mockups https://github.com/oncokb/oncokb/issues/2580
• Todo list:
  • [ ] Finalize design?
• Discussion result: we probably want to have separate columns for single and multiple icons. And we may need some new headers when having multiple icons (e.g. each column has a icon, different icons to represent Oncogenic, Therapeutic Levels, Diagnostic Levels and Prognostic Levels)
• Assignees: Hongxin

1.5 Grouped columns for the annotation column (superseded by 2.4)

• Goal: Figure out a way to have grouped columns for the annotation column (Annotations > (OncoKB, cancerhotsots etc).
• Ticket: Grouped columns in mutations table https://github.com/cBioPortal/icebox/issues/189
• Discussion result: this will be part of grouped mutation columns(2.4).

1.6 Improve sorting (superseded by 2.4)

• Goal: we can sort and filter individually per column/annotation
• Ticket:
  • Improve annotation column https://github.com/cBioPortal/cbioportal/issues/8522
  • Grouped columns in mutations table https://github.com/cBioPortal/icebox/issues/189
• Discussion result: this will be part of grouped mutation columns(2.4).

2. Column menu

2.1 Add Clinical Attributes to Mutations Column Menu

• Ticket: Add Clinical Attributes to Mutations Column Menu https://github.com/cBioPortal/cbioportal/issues/8657
• Todo list:
  • [x] Widen header + add tooltip to column header
• Status: DONE!
• Discussion points: https://github.com/cBioPortal/cbioportal/discussions/8659
• Assignees: Rajat

2.2 Filtering per column

• Ticket:
  • Add column-based filters for mutation tables https://github.com/cBioPortal/cbioportal/issues/8713
  • Add link to filtered study view in results view mutation table https://github.com/cBioPortal/cbioportal/issues/8802
• Todo list:
  • [x] Add numerical filtering
  • [x] Add categorical filtering
  • [x] Performance enhancements
  • [ ] Add link to filtered study view
• Status: Additional feature in progress
• Discussion points: https://github.com/cBioPortal/cbioportal/discussions/8659
• Assignees: Rajat

2.3 Add column number in menu button and tabs

• Ticket: no (mockup slides 24 and 25)
• Todo list:
• Status: DONE!
• Assignees: Rajat

2.4 Grouped mutation columns

• Ticket: Support grouped columns in LazyMobxTable: https://github.com/cBioPortal/icebox/issues/192
• Todo list:
  • [ ] Add an option to group columns
  • [ ] Grouped columns should be rendered together
  • [ ] Grouped columns should support having a group header
  • [ ] Ideally a group may have other groups, so support for multi level nested groups would be nice.
• Discussion points:
  • Current design (mockup slides 25) is too redundant on group name, e.g. "Mutation Event" is in every column selection but it's too long to be there
    • some ideas:
    • slide 25:
    • slide 29:
• Discussion result: good to have it! Before having the final UI design we could spend some time on data structure
• Assignees: Onur

3. Store settings

3.1 Store user settings

Keep track of what columns were selected

• Ticket:
  • Store user settings on what columns are shown for patient view and mutations tab separately https://github.com/cBioPortal/cbioportal/issues/8521
  • Improve annotation column https://github.com/cBioPortal/cbioportal/issues/8522
  • Point 4 in https://github.com/cBioPortal/cbioportal/issues/8716
  • slides 32
• Discussion result: we could store user settings in memory and apply them when switching genes, but not apply for new queries or different studies.
• Status: DONE!
• Assignees: Rajat

3.2 Add "reset to default" button based on app configuration (related to 3.1)

• Ticket: Point 3 in https://github.com/cBioPortal/cbioportal/issues/8716
• Todo list:
  • [x] Finalizing design
• Status: DONE!
• Assignees: Rajat

[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.

[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.