sourmash compute csv output with metacodeR

[FrAoJm]

Hi,
hope all of you are good.
I used Sourmash compute with a collection of bacterial isolates in two experiments (1 with only one type of bacteria) and another one with several types of bacterias).
I get the csv files and imported as distance matrix to R.

I would like to perform a nice plot of them using metacoder, but honestly, have no clue how to star with it. Everything I found is for taxonomical LCA. Should I perform some kind of LCA with my data?

I would appreciate any help with it!
Thanks!

[ctb]

hi @FrAoJm do you have an example of the kind of plot (screenshot, whatever) that you want to produce? metacoder does require taxonomy information so you'd probably want to run a sourmash lca summarize on your signatures using the LCA databases downloadable here, as in this tutorial.

Please see grunwaldlab/metacoder#246 for another person who did something similar!

Happy to help, please keep asking questions :)

[FrAoJm]

Thank you @ctb! Ideally, the PI would like to produce something like; https://www.microbiologyresearch.org/docserver/ahah/fulltext/mgen/6/4/mgen000347-f1_thmb.gif

But in summary, it would be something with the relationship between strains of the same bacteria. I will try to perform LCA with the databases and follow the tutorial. Then I will try to focus on the relationship only in the branch of my samples.

I will take a look to grunwaldlab/metacoder#246 to see what they did.

Thank you again! Regards!

[ctb]

see code in #2041, and also in STAMPS 2022 tutorial - here