biocore / biocore/empress

Warn the user in the barplot legends about tips that have no feature metadata / are not in the BIOM table

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#362 0 comments 0 reactions 0 assignees View on GitHub
barplots feature request
Dominant language
JavaScript
Stars
56
Forks
32
PR merge metrics
No merged PRs in 30d

Description

A warning is shown for continuous barplot legends when some tips have non-numeric feature metadata for the field:

![image](https://user-images.githubusercontent.com/4177727/91626500-70ff4380-e964-11ea-9054-db924f640972.png)

(this is with a test version of the MP dataset where I replaced a few tips' `Confidence` values with non-numeric junk.)

It would be good to also show a warning about tips that do not contain any feature metadata (for which no bars are drawn in a feature metadata barplot, at least assuming that some color / length encoding is used), as well as about tips that are not present in the BIOM table (for which no bars are drawn in a sample metadata barplot, since we can't associate the tip with any samples). For 16S datasets, both of these cases will _probably_ only happen when `--p-no-filter-unobserved-features-from-phylogeny` is used.

The main challenge in making the code for this work will probably just be passing the information of "there were tips without [feature|sample] metadata" to the barplot layer objects.

Contributor guide

Open the contributing guide

Research direction

Start by tracing the existing continuous barplot legend warning and the barplot layer objects. Follow where missing feature metadata and missing BIOM-table tips are detected, then determine how that information reaches the legends. Done means the relevant barplot legends warn users about each missing-data case without changing the existing non-numeric metadata warning.

Written by the indexing model from the issue text.

Assessment

Tech stack
javascript
Domain
data-visualization
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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