I recently started analyzing data with qiime2-2022.8. To get alpha/beta diversity I ran the "qiime diversity core-metrics-phylogenetic" code. First columns of medata file
Metadata_YMKB_1.txt (918 Bytes)
qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table prepost-table.qza \ --p-sampling-depth 21224 \ --m-metadata-file Metadata_YMKB_1.txt \ --output-dir a_prepost/prepost-core-metrics-results/prepost-core-metrics-resultstype or
I also created .qzv files for faith_pd, shannon, and evenness data. These files looked fine. I have utilized @jbisanz very useful tutorial to visualize data in R: Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R
However, when I tried to create plots with faith_pd alpha diversity, I ran into errors. The issue is that faithpd (but not shannon or evenness) is an object with 3 variables. My SampleID column is a numerical list (not ID names) and my ID names are on the second column labelled "V2" with faith_pd data in a "V3" column. In the past, I've only had my ID names and also my "faith_pd" column. I don't have this issue with other alpha diversity .qza files. Has anyone run into this issue? If so, is there a work-around?
faithpd1 <-read_qza("faith_pd_vector.qza")$data %>% rownames_to_column("SampleID")
shannon <-read_qza("shannon_vector.qza")$data %>% rownames_to_column("SampleID")
evenness <-read_qza("evenness_vector.qza")$data %>% rownames_to_column("SampleID")