Although we currently provide API documentation for the available commands in this package, we don't provide a quickstart tutorial that describes how to run these commands together.
We should make a brief quickstart guide in the README.md file that shows how to download some example flu data (maybe from the cartography project?), run pathogen-distance on the alignment, run pathogen-embed on the distances and alignment, visualize the embedding figure, inspect the embedding output (head mds.csv), inspect the soon-to-come pairwise distance plot to pick a distance threshold for clustering, run pathogen-cluster, and inspect the cluster results (head cluster_mds.csv).
It would be even more helpful to show how to merge the cluster/embedding table with metadata from a Nextstrain analysis and visualize the results in Nextstrain, but I think that's for a separate future issue.
Although we currently provide API documentation for the available commands in this package, we don't provide a quickstart tutorial that describes how to run these commands together.
We should make a brief quickstart guide in the
README.mdfile that shows how to download some example flu data (maybe from the cartography project?), runpathogen-distanceon the alignment, runpathogen-embedon the distances and alignment, visualize the embedding figure, inspect the embedding output (head mds.csv), inspect the soon-to-come pairwise distance plot to pick a distance threshold for clustering, runpathogen-cluster, and inspect the cluster results (head cluster_mds.csv).It would be even more helpful to show how to merge the cluster/embedding table with metadata from a Nextstrain analysis and visualize the results in Nextstrain, but I think that's for a separate future issue.