Trait Distribution Chart Field!

[laceysanderson]

Metadata

• Issue #66

• [x] I feel this PR is ready to be merged.
• [ ] This PR is dependent upon nothing

Documentation:

• [x] My code follows the code style of this project.
• [ ] My change requires a change to the documentation.
• [ ] I have updated the documentation accordingly.

Description

We need a field to embed the trait distribution plot on trait, germplasm and project pages.

Pertinent information from user feedback:

• Trait pages where there a multiple methods/units used for a single project: show all methods/units in stacked charts for comparison. This should only be within a single experiment.

This PR creates a single field (hp__phenotypic_variability) which is automatically included on germplasm (base table: stock), experiments (base table: project), and traits (base table: cvterm). This field will show a trait distribution plot and selector fields.

Specifically,

• Trait Pages: Trait matches the page, experiment is chosen from drop-down.
  • If only one experiment should be automatically shown: [fresh]/Trait/2653829
  • If there is more then one method/experiment, they should all be shown: [fresh]/Trait/2653826
  • Both violin and multibar charts should work: [tripal]/bio_data/6 (Violin) and [tripal]/bio_data/3 (Multibar; bad data example 🤷‍♀️ )
• Project Pages: Experiment matches the page; trait is chosen from drop-down.
  • If only one trait should be automatically shown:
  • If there is more then one method/experiment, they should all be shown: [tripal]/bio_data/2
  • Both violin and multibar charts should work: [tripal]/bio_data/2
  • Only traits with data should be in the drop down: [fresh]/study/2653525 (should not include Flower/Stem/Root Height).
• Germplasm Pages: Both Experiment and Trait Drop-downs.
  • Only includes experiments/traits for which this germplasm has data: [tripal]/bio_data/245 (No lorem ipsum)
  • If germplasm has data for only one trait then it should be automatically shown:
  • If there is more then one method/experiment, they should all be shown: [tripal]/bio_data/10 (Lorem ipsum)

Testing?

• [x] I tested on a generic Tripal Site
• [x] I tested on a KnowPulse Clone
• [x] This PR includes automated testing

The most recent version of this code is on both dev tripal and fresh. You can test using

• the above linked pages
• [tripal]/admin/content/bio_data any Trait, Germline Variant or Project content.
• [fresh]/admin/content/bio_data any Trait, or Study (only AGILE should show chart)` content.

Known Issue: There is a known issue with the chart not fitting well in the page. This is a problem with the chart and not the field and is due to it being a fixed size. This problem will be fixed in a later issue.

[reynoldtan]

Tested all items in this PR and they all worked 👍 , with just a few minor fine adjustments/suggestions below.

1. With the chart issue being a fixed width, I would suggest to just center the chart in the pane. This way it is not too obvious that the chart has width limitations.

2. The violin plot has a hover event that shows a window with extra information about a figure. However, the barchart does not have this and also, in the violin plot, the window appears in the figure legend text and not next to the pointer/figure as you would expect.

3. For collection method, on page load, they are all collapsed showing only the title of each method. Could the first item in the list be expanded? Just an added cue that those links contain more information and here I am showing you the first.

4. When clicking on the left hand side navigation, the content area seems to pulsate several times.

The x axis can be cluttered and unreadable. I believe this will be addressed by fixed width issue. I just want to include this observation in this review.