search

blekhmanlab / biomehorizon

Plot microbiome time series in parallel
Other
24 stars 2 forks source link

otudata has duplicate OTU rows #13

Open yasminhilliam opened 2 years ago

yasminhilliam commented 2 years ago

Hi, I'm super excited to generate some figures with this package, it's exactly what I've been looking for. However, I'm running into some issues early on with importing my data. I have generated a feature table TSV from QIIME2 which has unique sample IDs as column names and ASV feature IDs as row names, with counts for each (646 obs. of 48 variables). However, when I run paramList <- prepanel(otudata = otu, metadata = meta, subj = "subject1") I receive the following error:

Error in prepanel(otudata = otu, metadata = meta, subj = "GESCF14") : 'otudata' has duplicate OTU rows

I have extracted the row names into a list:

otulist <- rownames(otu) chr [1:646]

and then checked for unique values

unique(otulist)

R tells me that there are 646 unique values. So I am not sure where this error is being introduced. Can you offer any advice? Thanks in advance!

isaacfink21 commented 2 years ago

Hi @yasminhilliam, apologies for the late response. This error will happen if there are more rows in your otudata set than unique OTU IDs. Do you have any extra rows that don't correspond to sample reads for an OTU?

jspychalla commented 12 months ago

Hi, I am running into a similar error the dimensions of my otu table are 63 by 3497. My unique(otulist) outputs 63 unique OTU names. I do not see any extra rows in my dataframe when I view it in R. Could something else be giving me this error?

Super excited about this package as well it is exactly what I have been looking for