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ukaraoz / microtrait

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hclust_rows = clusters_traitmatrix[[1]] #6

Open MRMHmdoynova opened 1 year ago

MRMHmdoynova commented 1 year ago

Hi there,

Thank you very much for creating the package. There are a lot of good functions in it and we definitely will employ it in our analyses. I was just wondering did anyone happen to get to the steps prior generation of guilds? What hclust_rows is supposed to mean and how do I calculate it, considering the code in the previous steps? Can someone please, show an example?

nguilds = seq(2, nrow(trait_matrixatgranularity3), 2) hclust_rows = clusters_traitmatrix[[1]]

maov_results_list = parallel::mclapply(2:length(nguilds), function(i) { v = cutree(hclust_rows, nguilds[i]) genome2guild = data.frame(guild = factor(v)) rownames(genome2guild) = names(v) adonis_results = vegan::adonis2(distance ~ guild, data = genome2guild, perm = 1) adonis_results }, mc.cores = floor(0.8*detectCores()))

Thank you very much for your help!

Best Regards,

Malina

johannalheureux23 commented 3 months ago

Hi @MRMHmdoynova - did you ever figure this out? I have the same exact question!

Best, Johanna

ukaraoz commented 3 months ago

Hi @MRMHmdoynova, could you share your inputs to the function please?