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seattleflu / augur-build

the (in development) augur build for understanding influenza dynamics in Seattle
https://seattleflu.org
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Coloring scipts #30

Closed miparedes closed 5 years ago

miparedes commented 5 years ago

This PR refers to #17

Creates two different coloring scripts:

assigns_coloring_to_census_tract_seattle_only.py is, as the name suggests, Seattle specific. It takes in lat_longs.tsv as --coordinates, a --label which for seattle would be 'location' , and a file name as --output and divides up the Nextstrain color ramp using the latitudes and then lighten/darkens based on the longitudes. Outputs a .tsv file

assigns_coloring_using_tsne.py is a more generalizable coloring script that takes in lat_longs.tsv as --coordinates, a --label (like "region", 'country', 'location' etc.) and and a file name as --output. The script then uses 1D t-SNE on lat/long to assign colors. Outputs a .tsv file. Can also be used for Seattle by using the optional input --city and stating "Seattle" which will restrict the census tract bounds to city limits.

trvrb commented 5 years ago

I've updated these scripts a bit and rebased on top of master.