bokulich-lab/fermdb

fermdb's Issues

Update contributors for v 1.0

We will have a few more contributors to add (once they approve).

I can put in a PR but I see that the contributors are listed in two files. Should I edit index.html or index.Rmd?

ENH: map color scale

I have some suggested improvements to the color scale on the map.

1. The color bar is very long with too many tick labels. I suggest shortening the bar and making fewer tick labels.
2. The tick labels are also ranges, which makes for a very verbose legend. Could a single number be used for each label?

Create a simple dashboard

We need a simple dashboard which will take the data contained in the CSV/TSV file stored in this repository and generate a simple visualization (e.g. a pie chart of food types).

The dashboard needs to be deployed to GitHub pages: #2.

Renaming FermDB .xlsx file and providing other formats for the user

It might be good to rename the Fermented_food2.xlsx conatining the FermDB raw data file to something more meaningful. I would suggest FermDB or FermDB_data. It would also help to provide it in some additional format like tsv.

Set up GitHub action to publish the dashboard to GitHub Pages

Requirement criteria:

• action runs only on PR merge
• action builds the updated dashboard and deploys it to GitHub Pages

For some inspiration on deploying GitHub Pages, feel free to check out one of our JupyterBook repos: https://github.com/bokulich-lab/DataVisualizationBook

Create a json file with all the food ontologies

We need a single json file which will contain all the levels of the food ontology prepared by @rhernandvel.

license

We should put the dashboard and database under a specific license.

In FermDB this license should also be mentioned on the "About" tab, and next to the data download at the top of the "Data" tab.

I would lean toward CC-BY-SA-4.0 for the database and BSD-3 for the code. The CC-BY licenses are explicitly not recommended for software and BSD-3 is written specifically for software. Otherwise a single license would be easiest (and I am open to suggestions!)

@ZuzanaSebb @misialq any thoughts on this?

Graphs tab: add a column title?

The tiles on the left side of the "Graphs" page are very attractive! But it could be confusing to naive readers what these refer to.

Would it be possible to add another tile at the top of the column that says "Annual Production Volume"?

errors in dashboard data

There are errors in the country names (have not thoroughly checked other columns yet). Many countries are missing letters, especially "a" and "l" (e.g., "Coombi" instead of "Colombia").

The raw xlsx in the docs directory does not appear to be affected, so I suspect that some data importing or processing step is introducing errors in the dashboard data.