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globaldothealth / list

Repository for Global.health: a data science initiative to enable rapid sharing of trusted and open public health data to advance the response to infectious diseases.
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[VOC VIZ] Create New VOC Map View #2041

Closed rkassa closed 2 years ago

rkassa commented 3 years ago

Description:

b 1 1 7

rkassa commented 3 years ago

This would be a new map view from the main nav, called "Variant Public Reporting" for now:

image

Mougk commented 3 years ago

I would suggest to the right of coverage. Maybe use variant reporting rather than variant public reporting (shorter).

joe-brilliant commented 2 years ago

Recapping notes from sync / slack cc @rkassa @outbreakprepared

-- Add the following fields to hover state:

--

joe-brilliant commented 2 years ago

@rkassa @outbreakprepared @ryanfitzgerald19 let's review the latest version and go through these items above and determine a go-live date to back out from as the top agenda item for tomorrow's sync

maciej-zarzeczny commented 2 years ago

Hi @ryanfitzgerald19, I'm having trouble understanding this bullet point: Group Variants of Concern and Variants of Interest in menu sections, with VoCs first, and including the Greek names for VoCs (e.g. Delta) as defined by the WHO. @joe-brilliant said that you could help me understand that.

Currently all VoCs from the Google spreadsheet are in one big dropdown (see screenshot below). The order in which those VoCs appear is the same as the order in the spreadsheet. Please let me know how do you think it should be split into sections? Maybe creating separate dropdown for VOIs? It is possible to sort all VoCs and VoIs coming from spreadsheet into different categories, I'm just not sure how to display them on the map.

Screen Shot 2021-09-28 at 13 55 15

Also I'm not sure about this one: add some basic logic to merge all the Delta "sub"variants. Can you also explain it a little bit more?

Thank you in advance!

joe-brilliant commented 2 years ago

Hi @ryanfitzgerald19 @outbreakprepared @Mougk bumping this last comment / question from @maciekz1996. Could you help provide some feedback and guidance to move this forward next week while I'm out? I like the idea of separate dropdowns for Variants of Concern and Variants of Interest as a simple and intuitive first approach. I think we will also need input to decide on what should be included in the popups, latest prototype here: http://dev-vocviz-sample.s3-website.us-east-2.amazonaws.com/

joe-brilliant commented 2 years ago

@maciekz1996 @rkassa here are the lookup tables, is this all we need? https://www.dropbox.com/s/ivnus4scvg2ydbh/mapbox-boundaries-v3_3.zip?dl=0

joe-brilliant commented 2 years ago

@maciekz1996 @rkassa for the Google API issue, would making the Gsheets visible to all be another solution? I see no problem with that

Mougk commented 2 years ago

Thanks all -- looking v nice. below a list from @outbreakprepared (David) and I:

Legend (rather than checked use below)

In pop up:

joe-brilliant commented 2 years ago

Thanks @Mougk and @outbreakprepared, adding my notes from slack as well::

maciej-zarzeczny commented 2 years ago

@joe-brilliant @Mougk @outbreakprepared Thank you for the feedback, I am now working on fixing things mentioned above. I will keep you updated. @Mougk If you could prepare explainer texts and post them here that would be very helpful.

maciej-zarzeczny commented 2 years ago

@joe-brilliant @Mougk I fixed most of the things mentioned above. I don't understand how

Pango Lineage rather than VOC (Delta for example includes not just B.1.617.2 but also AY.4 and others). We can include the VOCs in parentheses behind the Pango Lineage name as a compromise for now.

and

We still need to add the Greek name equivalents to the VoC’s

should work. Can we discuss it on today's call?

joe-brilliant commented 2 years ago

Thanks @maciekz1996 great progress; yes let's plan to discuss on today's sync

beoutbreakprepared commented 2 years ago

Explainer note: "This map indicates the status of reporting of variant-related data in a publicly accessible locally managed resource"

joe-brilliant commented 2 years ago

thanks @beoutbreakprepared I'll weave this into an updated master help text module for Maps and post below

@Mougk @beoutbreakprepared there was some discussion and requests for clarification from @maciekz1996 on naming conventions. Is your recommendation that we list the lineages first, and the greek letters in parentheses?

e.g.

B.1.1.7 (Alpha) B.1.351 (Beta) P.1 (Gamma) B.1.617.2 (Delta) AY.4 (Delta)

If so, we should prob add a column or another worksheet so that occurs dynamically with future updates. Could you add those fields to the spreadsheet for the VOCs and VOIs we want to include? Also we should we put in this (Greek) alphabetical order ^ ?

maciej-zarzeczny commented 2 years ago

@joe-brilliant @Mougk @beoutbreakprepared I added the changes as suggested above, also the styles were updated to match the rest of the maps app. You can take a look at the newest version here: http://dev-map.covid-19.global.health/#country

I had to change spreadsheet's structure in order to include WHO labels next to Pango lineages. You can see the updated spreadsheet here: https://docs.google.com/spreadsheets/d/15-2lbrYHHL0zFYc9kzS7_m6CCV5BkBCUeg9ifTHbRos/edit#gid=71298198

You can edit the values and add new rows. Only the column headers can't be updated (the bold ones) and spreadsheet's structure as I use this structure in the code to fetch data.

joe-brilliant commented 2 years ago

thanks @maciekz1996! can you copy and paste the current Map help text in a comment? I will then edit and send back proposed changes directly. I can't seem to copy and paste it from the Map app itself. Also think we should link to Google sheet in the help text as view only. Can we hide the other tabs?

Only other notes are that it looks like Beta and Gamma should be flipped in order, and that perhaps we can arrange the text in the main nav box so it's not as wide (matches look/feel/size of other map views)?

@Mougk @beoutbreakprepared any feedback on the map or spreadsheet?

maciej-zarzeczny commented 2 years ago

@joe-brilliant Here is the help guide text:

These geospatial data visualisations allow you to explore our COVID-19 line-list dataset through a few different views:

Country View: Click on a country to see available line-list data in that country, and click through to see corresponding filtered results on G.h Data. You can also use the left-hand navigation to search or select a country, and view available data for Variants of Concern using the filters. Darker colours indicate more available data. (Please note: not all Variant of Concern data are downloadable. Please see our FAQs and Data Acknowledgments for more info.)

Regional View: Click on extrusion to see available line-list data in that region, and click through to see corresponding filtered results on G.h Data. Taller extrusions indicate more available data. Records that do not include regional metadata are labeled as "Country, Country" (e.g. "India, India"). Please see our FAQs for more info.

Coverage Map: This view illustrates available line-list COVID-19 case data in the Global.health database in a given country as a percentage of total cumulative case data as indicated by the Johns Hopkins University COVID Resource Center. Darker colours indicate more available line-list data. Totals are updated daily.

I flipped the order of Gamma and Beta variants (it can be done directly from the spreadsheet).

I also updated the styling of the new map so that it matches current map application better as you mentioned. The newest version can be seen here: http://dev-map.covid-19.global.health/#voc

joe-brilliant commented 2 years ago

Thanks @maciekz1996 one quick note: The "C" and "I" in the menu toggle should also be capitalized. I'll send over updated copy shortly

joe-brilliant commented 2 years ago

Thanks @maciekz1996. Suggested updated Map Help copy below. Please ensure all the existing and new hyperlinks are included. (@Mougk @beoutbreakprepared I elaborated on the VoC portion a bit to give a bit more context and added a link to the SS, please take a look and revise/approve)

Country View: Click on a country to see available line-list data in that country, and click “Explore Country Data” to view and download corresponding filtered results of data for that country. You can also use the left-hand navigation to search or select a country. Darker colours indicate more available line-list data.

Regional View: Click on a circle to see available line-list data in that region, and click “Explore Regional Data” to view and download corresponding filtered results of data for that region. Larger, darker circles indicate more available line-list data. Records that do not include regional metadata are labeled as “Country, Country” (e.g. “India, India”). Please see our FAQs for more info.

Coverage Map: This view illustrates available line-list COVID-19 case data in the Global.health database in a given country as a percentage of total cumulative case data as indicated by the Johns Hopkins University COVID Resource Center. Darker colours indicate more available line-list data. Totals are updated daily. The availability of publically-reported line-list data varies substantially by country. Please see our FAQs for more info.

Variant Reporting: This view indicates the status of reporting for variant-specific COVID-19 genomic sequencing data in a publicly accessible locally managed resource by country, as indicated by the color-coded legend. Use the navigation module to select a Variant of Concern or Variant of Interest (as defined by the WHO). Click on a country to see the latest date checked, number of reported breakthrough infections (if available), and access the Public Source URL. You can also view the live version of the underlying Google Sheet here, which the G.h team updates periodically. Please note that Variant Reporting data is currently not included in the line-list database.

maciej-zarzeczny commented 2 years ago

@joe-brilliant @Mougk (fyi @marlenachroscicka) I added all the changes, they can be seen here: http://dev-map.covid-19.global.health/#voc

I also added PR containing all those changes to viz repository: https://github.com/globaldothealth/viz/pull/112. If everything looks and works as expected, @rkassa could just merge this PR and deploy to production.

joe-brilliant commented 2 years ago

Thanks @maciekz1996 looking good! I don't see the new help text in place yet, can you ping when that's up? One small cosmetic note: it looks like the "V" and "C" and "V" and "I" in the nav module may not be fully aligned. Can we tighten that up? cc: @Mougk @beoutbreakprepared for any other final feedback before @rkassa's push this to production along with the Regional View circle / pop up fix (i.e. #2201 )

maciej-zarzeczny commented 2 years ago

@joe-brilliant That's my bad, the new help text was added on Friday but I didn't deploy it correctly to AWS do that's the reason you couldn't see the updated content. I'm working on this right now. I also reached out to @rkassa as I'm experiencing one issue during deployment process. When it comes to the letters being misplaced, I'm not sure if I understand this correctly. I think it would be best to go through it on today's call

joe-brilliant commented 2 years ago

Closing for now to be revisited post React deployment