Map AtlantECO samples

Plot sample locations from all AtlantECO flagship studies.

AtlantECO brings together studies of the Atlantic Ocean and its ecosystems. Fetch samples from all its flagship studies and explore their locations on a map.

Edit and run the cells in order. The first visit may take a minute to load.

Find the studies

A super-study groups related MGnify studies. Show the first 20 AtlantECO flagship studies. Change 20 to see more:

Get the samples

Collect every page of samples for each flagship study. A sample can belong to several studies, so keep one record per sample accession. Unavailable studies are reported and skipped.

Prepare the coordinates

Latitude and longitude are stored in the sample metadata as text. Convert them to numbers and omit samples with missing or out-of-range coordinates.

Draw the map

Zoom in and click a marker to see the sample accession, the AtlantECO studies it belongs to, and its coordinates. Samples collected at the same location share a marker position.

Try changing the marker colour or radius, then run the map cell again.

Running this code in your own environment

Install the packages from a terminal:

python -m pip install pandas requests folium

Run the Python cells in a notebook to display the map. In a Python script, use sample_map.save("atlanteco.html") and open that file in your browser.