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Volcano plot, possibly as gene selection interface

See original GitHub issue
  1. We know that users want more of a sense of the overall structure of the genes in the dataset
  2. We know that users want to see more than 15 results for diffexp
  3. We frequently only surface markers for one of the diffexp populations rather than both
  4. Users are used to using volcano plots
  5. Heatmaps are gigantic and unwieldy

Fig. 1 via:


Fig. 2 via:


Rough proposal: cellxgene shows a volcano plot on diffexp, perhaps immediately and as a result of selecting diffexp on 2 categorical metadata labels! This then serves as an intermediary step to selecting the genes to return, which are then populated in a gene list in the right hand side bar.

Fig 1 would seem to show selection cutting off small y axis values, while Fig 2 does the same but also allows the user to remove symmetrically from the center.

We could also add a voronoi overlay to hover and show point labels

Big open question: how do users want to accomplish the selection?

  • Could be multiple boxes
  • Could be a lasso
  • Could be 2 or 3 continuous sliders: min value y axis, distance from centerline negative, distance from centerline positive

cc @sidneymbell @ambrosejcarr

A big thank you to Dana Pe’er’s lab at Memorial Sloan Kettering for pointing out this plot and process.

Issue Analytics

  • State:open
  • Created 4 years ago
  • Reactions:1
  • Comments:6 (5 by maintainers)

github_iconTop GitHub Comments

atarashanskycommented, Mar 20, 2022

Managed to turn this around quickly. Released in excellxgene v2.5.3!

atarashanskycommented, Mar 19, 2022

Thanks @colinmegill for pointing me to this backlogged issue. Love the idea, and it’s pretty straightforward to implement in excellxgene. The specific implementation details might be dependent on how I’ve rearranged the backend (mainly, how the various data types and metadata are saved on the server, read by requests, etc), so looping in this feature to cellxgene will probably require updating the backend as well.

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