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biocore / emp

Code repository of the Earth Microbiome Project.
http://www.earthmicrobiome.org
BSD 3-Clause "New" or "Revised" License
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map of the earth containing location of all samples (and sub-maps colored by sample site) #2

Closed gregcaporaso closed 7 years ago

douginator2000 commented 12 years ago

Sounds like an interesting project - can you elaborate on the sub-maps colored by sample site? Sounds like a good project for Google Maps or Google Earth.

gregcaporaso commented 12 years ago

I think we need Rob's input on this, but I think the idea is that you could zoom into a particular view and see all of the sample sites within one location. This does sound achievable within Google Maps/Earth and having an interactive map that was embedded in the EMP login page so user's don't need to be logged in would be great.

douginator2000 commented 12 years ago

K, we'll wait for additional feedback.

gregcaporaso commented 12 years ago

Rob is traveling with bad internet right now, so I think the way to go is to start with a google maps/earth approach with the ability to embed that in an web page, and with the ability to get multiple levels of resolution (e.g., zoomed out to the full planet shows cities, zoomed in shows particular sample sites). Jack, do you agree that this would be a good way to go?

Greg

On Mon, Jul 30, 2012 at 3:32 PM, douginator2000 reply@reply.github.com wrote:

K, we'll wait for additional feedback.

Reply to this email directly or view it on GitHub: https://github.com/EarthMicrobiomeProject/isme14/issues/2#issuecomment-7379262

gilbertjack commented 12 years ago

yes this is the way to go - currently this is already available on the GESD for individual samples and groups of samples for us - so yes I like this.

But it is also necessary to have the piechart or whatever that shows samples by the environment origin, so that people can select groups of samples from marine or human sites. Would be nice to imbed in each level sub levels as per the ontologies. i.e. marine-sediment or human-skin.

gilbertjack commented 12 years ago

Daniel Smith - Can you have a go at placing specifically Doug Wendel's google maps version of the EMP sampling locations on the front page of the EMP website - connect with Doug on this as he already has the flat file.

This will need to be linked to the GESD database so that is is automatically updates - not sure how easy this is?

What would also be great is if we could visualize the number of samples for each location on this map (similar to what DanS did before) but in this case it will be dynamic - as in you can zoom in and out. This assumes that there are sometimes multiple samples at the same Lat:Long - which I know to be the case.

Also possibly link to data from the entry on the map - i.e. (from Greg) click on a sample location and link to the project record, and/or sample records for that sample/location. with option to download the data.

douginator2000 commented 12 years ago

Hey guys,

It's already linked to the database so it's always live data. Let me know how I can help - I assume this will be on the main EMP site and not our portal correct?

On Thu, Aug 2, 2012 at 12:46 PM, gilbertjack reply@reply.github.com wrote:

Daniel Smith - Can you have a go at placing specifically Doug Wendel's google maps version of the EMP sampling locations on the front page of the EMP website - connect with Doug on this as he already has the flat file.

This will need to be linked to the GESD database so that is is automatically updates - not sure how easy this is?

What would also be great is if we could visualize the number of samples for each location on this map (similar to what DanS did before) but in this case it will be dynamic - as in you can zoom in and out. This assumes that there are sometimes multiple samples at the same Lat:Long - which I know to be the case.

Also possibly link to data from the entry on the map - i.e. (from Greg) click on a sample location and link to the project record, and/or sample records for that sample/location. with option to download the data.

Reply to this email directly or view it on GitHub: https://github.com/EarthMicrobiomeProject/isme14/issues/2#issuecomment-7464461

Doug Wendel, PRA University of Colorado at Boulder Department of Chemistry and Biochemistry Knight Lab

gregcaporaso commented 12 years ago

@dansmith01: Can you help @douginator2000 get this embedded in the main EMP website?

@douginator2000, is there a link that is currently accessible that doesn't require logging in? If so, can you post that here?

gilbertjack commented 12 years ago

@dansmith01 and @douginator2000 it would also be nice to include on this dynamic map a visual representation of the number of samples present at that location - I know I said this before, but I am making a point of it. :-)

dansmith01 commented 12 years ago

@douginator2000 - Can you link me to the current version of the map? I'll look into incorporating it into the EMP website.

gilbertjack commented 12 years ago

Looking over the map it says that Fermilab sampling location is in Western China.....last time I looked it was near Argonne in Illinois.

@douginator2000 can you check with Gail and Sarah that the lat-longs are correct? This seems like a big job, but would be good to know if there are more errors.

gilbertjack commented 12 years ago

oh and there are some kelp soil metadata studies from Torsten Thomas somewhere in the middle of the South Atlantic - I wouldn't of thought we would find Kelp Soil there?

gilbertjack commented 12 years ago

Also some of the Dominguez Western Accultration studies of the human microbiome are in the Indian ocean.

I hope this is something we can fix, or people are making a bunch of silly mistakes in their latlongs.

gilbertjack commented 12 years ago

oh and a Coral Reef Microbiome samples just outside of Nanjing in China - apparently from Baross?

owenssm commented 12 years ago

I'll take a look into the latitude/longitudes.

Sarah

On Sat, Aug 11, 2012 at 4:05 AM, gilbertjack notifications@github.comwrote:

oh and a Coral Reef Microbiome samples just outside of Nanjing in China - apparently from Baross?

— Reply to this email directly or view it on GitHubhttps://github.com/EarthMicrobiomeProject/isme14/issues/2#issuecomment-7665175.

Sarah M. Owens, M.S. Technical Director, IGSB-NGS Core Argonne National Laboratory 9700 S. Cass Avenue Bldg. 202, Rm. A353 Lemont, IL 60439 Sarah.Owens@anl.gov 630.252.2101

gilbertjack commented 12 years ago

Thanks @owenssm

ackermag commented 12 years ago

Sarah I started doing this today and have repaired the kelp study. I am also renaming them with PI and sample type so that they are more intuitive for people who don't work with them daily

gregcaporaso commented 12 years ago

Any progress updates on this? Have lat/longs been repaired across the board?

owenssm commented 12 years ago

Yesterday Gail said she made some changes and had some luck.

On Tue, Aug 14, 2012 at 11:23 AM, Greg Caporaso notifications@github.comwrote:

Any progress updates on this? Have lat/longs been repaired across the board?

— Reply to this email directly or view it on GitHubhttps://github.com/EarthMicrobiomeProject/isme14/issues/2#issuecomment-7731182.

Sarah M. Owens, M.S. Technical Director, IGSB-NGS Core Argonne National Laboratory 9700 S. Cass Avenue Bldg. 202, Rm. A353 Lemont, IL 60439 Sarah.Owens@anl.gov 630.252.2101

gregcaporaso commented 12 years ago

Great. It would be worth checking whether the issues that @gilbertjack brought up have been resolved. Is someone on that? @douginator2000, is the map on the website updating as @ackermag makes changes?

ackermag commented 12 years ago

The lat longs are consistent with where the samples were obtained - all issues @gilbertjack have been addressed and more

ackermag commented 12 years ago

All updates are live

rob-knight commented 12 years ago

thanks!

On Aug 15, 2012, at 10:50 PM, ackermag notifications@github.com<mailto:notifications@github.com> wrote:

All updates are live

— Reply to this email directly or view it on GitHubhttps://github.com/EarthMicrobiomeProject/isme14/issues/2#issuecomment-7777307.

ackermag commented 12 years ago

Yes - everything is live I check as I update Gail

On Tue, Aug 14, 2012 at 10:29 AM, Greg Caporaso notifications@github.comwrote:

Great. It would be worth checking whether the issues that @gilbertjackhttps://github.com/gilbertjackbrought up have been resolved. Is someone on that? @douginator2000 https://github.com/douginator2000, is the map on the website updating as @ackermag https://github.com/ackermag makes changes?

— Reply to this email directly or view it on GitHubhttps://github.com/EarthMicrobiomeProject/isme14/issues/2#issuecomment-7731386.

Gail Ackermann Knight Lab UCB 596 University of Colorado Boulder

gilbertjack commented 12 years ago

Well done! Thanks all!

gregcaporaso commented 12 years ago

Great, so are we set to close this issue @douginator2000?

ackermag commented 12 years ago

I think this is done - manual curation will continue by study

douginator2000 commented 12 years ago

Thanks Gail.

On Aug 16, 2012, at 9:17 PM, ackermag notifications@github.com wrote:

I think this is done - manual curation will continue by study

— Reply to this email directly or view it on GitHubhttps://github.com/EarthMicrobiomeProject/isme14/issues/2#issuecomment-7806114.

dansmith01 commented 12 years ago

Where can I find the map showing this data?

cuttlefishh commented 8 years ago

@mortonjt -- Would you like to adapt your basemap code for this issue?

mortonjt commented 8 years ago

I'm game

mortonjt commented 8 years ago

Sorry. Got late into the conversion. Basemap is statically generated, so no zooming capabilities are enabled. I do have code to generate these data to highlight different metadata. Is that what is needed?

cuttlefishh commented 8 years ago

Yes, that's it exactly. Priorities are roughly:

  1. A 2D static map that we can color by any metadata variable, categorical or gradient. Basemap.
  2. A 2D dynamic map. `ili seems better suited than bokeh by first approximation.
  3. A 3D dynamic map. `ili or Emperor.

On that note, is Emperor capable of plotting metadata on any 3D array of points? This general functionality would be great. @ElDeveloper

ElDeveloper commented 8 years ago

Yes, this should be possible, the flag you would be looking for is -a, and you would need to have all numeric data in those metadata columns. I've never tried plotting latitude and longitude + PC1, but it should work, if not we can make it happen.

On (Dec-22-15|22:46), Luke Thompson wrote:

Yes, that's it exactly. Priorities are roughly:

  1. A 2D static map that we can color by any metadata variable, categorical or gradient. Basemap.
  2. A 2D dynamic map. `ili seems better suited than bokeh by first approximation.
  3. A 3D dynamic map. `ili or Emperor.

On that note, is Emperor capable of plotting metadata on any 3D array of points? This general functionality would be great. @ElDeveloper

Reply to this email directly or view it on GitHub: https://github.com/biocore/emp/issues/2#issuecomment-166815151

cuttlefishh commented 8 years ago

That would be awesome! I'll play around with that over break.

On Dec 23, 2015, at 11:47 AM, Yoshiki Vázquez Baeza notifications@github.com wrote:

Yes, this should be possible, the flag you would be looking for is -a, and you would need to have all numeric data in those metadata columns. I've never tried plotting latitude and longitude + PC1, but it should work, if not we can make it happen.

On (Dec-22-15|22:46), Luke Thompson wrote:

Yes, that's it exactly. Priorities are roughly:

  1. A 2D static map that we can color by any metadata variable, categorical or gradient. Basemap.
  2. A 2D dynamic map. `ili seems better suited than bokeh by first approximation.
  3. A 3D dynamic map. `ili or Emperor.

On that note, is Emperor capable of plotting metadata on any 3D array of points? This general functionality would be great. @ElDeveloper

Reply to this email directly or view it on GitHub: https://github.com/biocore/emp/issues/2#issuecomment-166815151 — Reply to this email directly or view it on GitHub.

mortonjt commented 8 years ago

Not sure about what would be the best way about this? Would you like IPython notebooks to plot all of the static maps - similar to what's going on in https://github.com/biocore/American-Gut?

Also, not sure if ili is designed to handle maps. And Emperor is definitely not built for that. I'd think that Google maps may be more appropriate. However, the API is has already been depreciated. So I'm not sure what the best alternative is - but there is a long list of options that can be explored.

ElDeveloper commented 8 years ago

Ah, this just reminded me, we've done some "interactive map stuff" in Platypus, that works with the IPython notebook, see here: http://nbviewer.ipython.org/github/biocore/Platypus-Conquistador/blob/master/ipynbs/Chasing_Platypus_via_MG-RAST.ipynb

On (Dec-26-15|12:55), mortonjt wrote:

Not sure about what would be the best way about this? Would you like IPython notebooks to plot all of the static maps - similar to what's going on in https://github.com/biocore/American-Gut?

Also, not sure if ili is designed to handle maps. And Emperor is definitely not built for that. I'd think that Google maps may be more appropriate. However, the API is has already been depreciated. So I'm not sure what the best alternative is - but there is a long list of options that can be explored.

Reply to this email directly or view it on GitHub: https://github.com/biocore/emp/issues/2#issuecomment-167362203

mortonjt commented 8 years ago

Whoa. That's awesome!

On Sat, Dec 26, 2015 at 6:25 PM, Yoshiki Vázquez Baeza < notifications@github.com> wrote:

Ah, this just reminded me, we've done some "interactive map stuff" in Platypus, that works with the IPython notebook, see here:

http://nbviewer.ipython.org/github/biocore/Platypus-Conquistador/blob/master/ipynbs/Chasing_Platypus_via_MG-RAST.ipynb

On (Dec-26-15|12:55), mortonjt wrote:

Not sure about what would be the best way about this? Would you like IPython notebooks to plot all of the static maps - similar to what's going on in https://github.com/biocore/American-Gut?

Also, not sure if ili is designed to handle maps. And Emperor is definitely not built for that. I'd think that Google maps may be more appropriate. However, the API is has already been depreciated. So I'm not sure what the best alternative is - but there is a long list of options that can be explored.

Reply to this email directly or view it on GitHub: https://github.com/biocore/emp/issues/2#issuecomment-167362203

— Reply to this email directly or view it on GitHub https://github.com/biocore/emp/issues/2#issuecomment-167374465.

cuttlefishh commented 7 years ago

Done by me (Luke T.) and Josh Lefler for EMP paper (Release 1).