How to plot a stacked barchart in phyloseq of relative abundances …
Jun 19, 2024 · I have a really basic phyloseq question which I annoyingly am unable to resolve. I have a phyloseq object (OTU table, taxonomy, and sample data) with 4 sample variables like …
r - How to creat a bar graph of microbiota data with one color for ...
Jun 29, 2020 · I have a Phyloseq object with my OTU table and TAX table. I would like to create a bar plot, at for instance family level, but families belonging to the same Phylum will be …
r - Phyloseq sample_data () and sample_names () not working to ...
Sep 4, 2020 · Phyloseq sample_data () and sample_names () not working to incorporate samples into phyloseq object Asked 5 years, 3 months ago Modified 7 months ago Viewed 3k times
phyloseq to csv, with selected rows and columns?
Jan 18, 2024 · For input to the r package SRS, I need a csv file with each column being a sample, and the rows being the taxa. I've been able to make similar outputs using psmelt but it …
Put phyloseq plots into a grid like formation - Stack Overflow
Jun 15, 2024 · I am writing on this forum because the phyloseq github issues page is not being answered and I need help with a very specific formating question. Ultimately, I want to have a …
R calculate most abundant taxa using phyloseq object
Jun 10, 2022 · R calculate most abundant taxa using phyloseq object Asked 3 years, 5 months ago Modified 3 years, 5 months ago Viewed 2k times
Removing spurious taxa from a phyloseq object - take 2
Mar 8, 2023 · Removing spurious taxa from a phyloseq object - take 2 Asked 2 years, 9 months ago Modified 2 years, 8 months ago Viewed 813 times
sam_data gets transformed into NAs and numerical values when …
Nov 2, 2022 · sam_data gets transformed into NAs and numerical values when using merge_samples phyloseq Asked 3 years, 1 month ago Modified 3 years, 1 month ago Viewed …
Converting existing data in R into Phyloseq OTU table
I have been attempting to "phyloseq-ize" my asv_table, asv_id, and metadata for a 16S analysis, created using qiime2 and uploaded to R using read.table(). I have been able to successfully …
I would like to plot (stacked bars) top 20 genus/family/species etc ...
Aug 17, 2023 · I have been trying to plot a bar plot on a phyloseq object, agglomerated by species and filtered (so n of ITUs = 542), but for only those top 20 genus that have the highest relative …