Hi Jordan,
Thank you for your reply. I understand that part but how is that part of the tutorial linked to this next part when we read in the files again?
phy<-qza_to_phyloseq(“v3v4-20190304-table-dada2-p-Phylum-only.qza”, “rooted-tree-v3v4-20190304-rep-seqs-dada2-p-Phylum-only.qza”, “V3V4-20190304-taxonomy.qza”, “20190304-sample-metadata-v3v4_nNC.txt”)
Here we are reading the table, the tree, the taxonomy, and the metadata in and convert it to a phyloseq object. Later, we use plot_bar(phy) to make the barplot. So I don’t understand how splitting using the code you wrote would affect phy since phy is acquired through reading the original files in and not the the split taxonomy file. That part was confusing to me.
So here’s what I did:
metadata<-read.delim(“20190304-sample-metadata-v3v4_nNC.txt”)
SVs<-read_qza(“v3v4-20190304-table-dada2-p-Phylum-only.qza”)
taxonomy<-read_qza(“V3V4-20190304-taxonomy.qza”)
taxtable<-taxonomy$data %>% as_tibble() %>% separate(Taxon, sep=";", c(“Kingdom”,“Phylum”,“Class”,“Order”,“Family”,“Genus”,“Species”))
tree<-read_qza(“rooted-tree-v3v4-20190304-rep-seqs-dada2-p-Phylum-only.qza”)
and then:
phy<-qza_to_phyloseq(“v3v4-20190304-table-dada2-p-Phylum-only.qza”, “rooted-tree-v3v4-20190304-rep-seqs-dada2-p-Phylum-only.qza”, “V3V4-20190304-taxonomy.qza”, “20190304-sample-metadata-v3v4_nNC.txt”)
but these two sets of codes seem separate since with phy, we seem to be reading the files in again and we are not using the taxonomy files that was made using:
taxonomy<-read_qza(“V3V4-20190304-taxonomy.qza”)
taxtable<-taxonomy$data %>% as_tibble() %>% separate(Taxon, sep=";", c(“Kingdom”,“Phylum”,“Class”,“Order”,“Family”,“Genus”,“Species”))
I am not sure how to link these two sets of codes to be able to include the split taxonomy file in my phy file.