Comments on: Microbial community segmentation with R https://www.polarmicrobes.org/microbial-community-segmentation-with-r/ Marine Microbial Ecology Sun, 04 Jul 2021 04:22:55 +0000 hourly 1 https://wordpress.org/?v=6.9 By: Jeff https://www.polarmicrobes.org/microbial-community-segmentation-with-r/#comment-470 Sun, 04 Jul 2021 04:22:55 +0000 http://www.polarmicrobes.org/?p=1894#comment-470 In reply to Sarah Amiri.

🙂

]]> By: Sarah Amiri https://www.polarmicrobes.org/microbial-community-segmentation-with-r/#comment-469 Sat, 03 Jul 2021 08:35:52 +0000 http://www.polarmicrobes.org/?p=1894#comment-469 The SOM examples you’ve provided on your lab site have helped me throughout 2021, thank you!

]]> By: Jeff https://www.polarmicrobes.org/microbial-community-segmentation-with-r/#comment-422 Mon, 22 Jul 2019 03:45:05 +0000 http://www.polarmicrobes.org/?p=1894#comment-422 In reply to Pitoon Kongnoo.

Pitoon, I’m not sure what code you’re referring to, all code is shown above. Not clear what you mean by “cluster in each map are not the same for each species”. You should have one map, and multiple clusters. The species should be distributed heterogeneously across clusters.

]]> By: Pitoon Kongnoo https://www.polarmicrobes.org/microbial-community-segmentation-with-r/#comment-421 Mon, 22 Jul 2019 03:34:51 +0000 http://www.polarmicrobes.org/?p=1894#comment-421 In reply to Jeff.

Hi, could you please share the code of the Segmentation of samples based on bacterial community structure and the data structure as in the Fig2. (previous post). I tried but the cluster in each map are not the same for each species

]]> By: Jeff https://www.polarmicrobes.org/microbial-community-segmentation-with-r/#comment-420 Fri, 19 Jul 2019 16:47:19 +0000 http://www.polarmicrobes.org/?p=1894#comment-420 In reply to Pitoon Kongnoo.

Yes, the kohonen package has received some updates since I published this post. The basic structure is the same, but some of the options are different for the commands. Check the kohonen documentation (specifically “help” for the som command).

]]> By: Pitoon Kongnoo https://www.polarmicrobes.org/microbial-community-segmentation-with-r/#comment-419 Fri, 19 Jul 2019 09:46:38 +0000 http://www.polarmicrobes.org/?p=1894#comment-419 ็Hi, I try to run this …..
som.model.edges <- som(edge.norm,
grid = som.grid,
rlen = 100,
alpha = c(0.05,0.01),
keep.data = TRUE,
n.hood = "circular",
toroidal = T)

Then got an error : Error in supersom(list(X), …) :
unused arguments (n.hood = "circular", toroidal = T)

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