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How to better display higher taxonomic unknown levels? #422

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antgonza opened this issue Oct 14, 2020 · 0 comments · Fixed by #487
Closed

How to better display higher taxonomic unknown levels? #422

antgonza opened this issue Oct 14, 2020 · 0 comments · Fixed by #487
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While discussing large trees and coloring by taxonomy, we realized that by default Q2 assigns "Unassigned" to sequences that didn't get an assignment, for example:
Screen Shot 2020-10-13 at 10 47 43 AM
and that Empress by default will fill missing levels with "Unspecified" and that this could become problematic when looking at higher levels, like this:
Screen Shot 2020-10-13 at 10 47 00 AM
as it merges the assignments that were "Unassigned" in level 1, with those without a classification at that specific level.

The questions are:

  1. What should we do about it? There were a couple of suggestions: (a) repeat the latests level available level in the missing ones, basically have "Unassigned" in all the levels or "k__Bacteria" if those are the highest level available; and/or (b) do 1 but also add the level we are looking in the label, from the example above: "Unassigned [L2]" in all the levels or "k__Bacteria [L2]"
  2. Should we do this by default or control via a parameter?
@fedarko fedarko mentioned this issue Dec 22, 2020
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@fedarko fedarko mentioned this issue Jan 19, 2021
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@fedarko fedarko mentioned this issue Feb 6, 2021
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fedarko added a commit to fedarko/empress that referenced this issue Feb 17, 2021
@fedarko
ENH: Implement ancestor fm retrieval in JS
e738361 
Closes biocore#473 and closes biocore#422.

Avoids having to store this stuff in the QZV, which will save
a lot of space. This does still involve storing the "expanded"
taxonomy for a given level all at once in memory, though -- I do
not think this will be horrendous, since it is not that much extra
data all things considered.
@fedarko fedarko mentioned this issue Feb 17, 2021
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kwcantrell pushed a commit that referenced this issue Apr 8, 2021
@fedarko
Use ancestor information in taxonomy feature metadata (only computing…
5b8a340 
… ancestor info in the JS interface) (#487)

* DOC: various match_inputs() comments/doc fixes

* ENH: Pass ordered tax col names to Empress JS #473

See docs enclosed for discussion vs. bool flag approach

* ENH: Implement ancestor fm retrieval in JS

Closes #473 and closes #422.

Avoids having to store this stuff in the QZV, which will save
a lot of space. This does still involve storing the "expanded"
taxonomy for a given level all at once in memory, though -- I do
not think this will be horrendous, since it is not that much extra
data all things considered.

* STY: prettify

* MNT: abstract fm retrieval func generation

still gotta test (manually then automatically) tho...

* TST: unbreak js tests

* TST: unbreak some of the python tests

not done yet

* TST: unbreak all python tests

* TST: abstract python taxcol checking

* STY: fix flake8 long lines

* STY: more flake8 fixes

* TST: test #473 special fm stuff in JS

* MNT: pass length fm retrieval through new funcs

for sake of future consistency. really shouldn't change anything,
behavior- or performance-wise

* BUG: Change max width to be in vw units, not vh

makes this slightly larger, i think

* PERF/DOC: Add note abt repeated work - fm barplots
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