search

biocore / empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis
BSD 3-Clause "New" or "Revised" License
45 stars 31 forks source link

Find LCA from selected features #427

Open wasade opened 3 years ago

wasade commented 3 years ago

It would be nice to be able to select a few tips and determine the LCA. In an empire plot, this can be particularly useful to help identify a portion of the tree driving a partitioning pattern.

fedarko commented 3 years ago

I can see how this would be useful! One sticking point may be that (to my knowledge at least) Empress doesn't really have a way of "selecting" more than one node at once yet -- we can highlight them via Empire plots, but under the hood all that's really happening is that the colors of all nodes representing a set of samples are being temporarily changed.

One solution might be adding a new tab for Selected Nodes or something that stores the history of all selected nodes, and has the ability to support things like filtering on this history to display the LCA on the tree (I'm imagining this working like a checklist of node names). This might tie in to some of the more detailed node selection/coloring work we've discussed, e.g. #417.

wasade commented 3 years ago

Going by sample selection could be cool too. For example, select two sets of points, and highlight on the tree the feature difference (or intersection or union) between the sets. And, or, the LCA of the difference

On Fri, Oct 16, 2020, 12:30 Marcus Fedarko notifications@github.com wrote:

I can see how this would be useful! One sticking point may be that (to my knowledge at least) Empress doesn't really have a way of "selecting" more than one node at once yet -- we can highlight them via Empire plots, but under the hood all that's really happening is that the colors of all nodes representing a set of samples are being temporarily changed.

One solution might be adding a new tab for Selected Nodes or something that stores the history of all selected nodes, and has the ability to support things like filtering on this history to display the LCA on the tree (I'm imagining this working like a checklist of node names). This might tie in to some of the more detailed node selection/coloring work we've discussed, e.g. #417 https://urldefense.com/v3/__https://github.com/biocore/empress/issues/417__;!!Mih3wA!WARmYdMZxmPNNpsT43vh3g1ADW_D1MAiR1QmIKwpLrtl-HC4fi5gbE3bDqRp1xP7VJnS$ .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/biocore/empress/issues/427*issuecomment-710480937__;Iw!!Mih3wA!WARmYdMZxmPNNpsT43vh3g1ADW_D1MAiR1QmIKwpLrtl-HC4fi5gbE3bDqRp1wqWUjuE$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AADTZMWGGSR3RU5S2QSU7BDSLCNMNANCNFSM4STUTSTA__;!!Mih3wA!WARmYdMZxmPNNpsT43vh3g1ADW_D1MAiR1QmIKwpLrtl-HC4fi5gbE3bDqRp105uM_xW$ .