{"action":"opened","issue":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/664","repository_url":"https://api.github.com/repos/joey711/phyloseq","labels_url":"https://api.github.com/repos/joey711/phyloseq/issues/664/labels{/name}","comments_url":"https://api.github.com/repos/joey711/phyloseq/issues/664/comments","events_url":"https://api.github.com/repos/joey711/phyloseq/issues/664/events","html_url":"https://github.com/joey711/phyloseq/issues/664","id":176271642,"number":664,"title":"Lost of OTU and taxonomic level labels using the tax_table function","user":{"login":"olar785","id":20408813,"avatar_url":"https://avatars.githubusercontent.com/u/20408813?v=3","gravatar_id":"","url":"https://api.github.com/users/olar785","html_url":"https://github.com/olar785","followers_url":"https://api.github.com/users/olar785/followers","following_url":"https://api.github.com/users/olar785/following{/other_user}","gists_url":"https://api.github.com/users/olar785/gists{/gist_id}","starred_url":"https://api.github.com/users/olar785/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olar785/subscriptions","organizations_url":"https://api.github.com/users/olar785/orgs","repos_url":"https://api.github.com/users/olar785/repos","events_url":"https://api.github.com/users/olar785/events{/privacy}","received_events_url":"https://api.github.com/users/olar785/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-09-11T23:22:26Z","updated_at":"2016-09-11T23:22:26Z","closed_at":null,"body":"Hi,\r\n\r\nI'm importing my OTU, taxonomic and sample tables as .csv files using the commands below. It works fine with the otu_table and sample_ table functions but when it gets to the tax_table function, my labels are lost and renamed sp1, sp2 for OTUs and ta1, ta2 for my taxonomic levels. Is it me doing something wrong or is there a glitch?\r\n\r\nN.B: I'm using R version 3.3.1 with the latest update for all packages\r\n\r\notu.rna<-read.csv(file.choose())\r\ntaxo.rna<-read.csv(file.choose())\r\nsites.rna<-read.csv(file.choose())\r\n\r\nrownames(sites.rna) <- sites.rna[,1]\r\nsites.rna<-sites.rna[,-1]\r\n\r\nrownames(otu.rna) <- otu.rna[,1]\r\notu.rna<-otu.rna[,-1]\r\n\r\nrownames(taxo.rna) <- taxo.rna[,1]\r\ntaxo.rna<-taxo.rna[,-1]\r\n\r\notu.rna = otu_table(otu.rna, taxa_are_rows = TRUE)\r\ntaxo.rna = tax_table(taxo.rna)\r\nsites.rna = sample_data(sites.rna) "}}
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