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 displayed with the …
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, 2 months ago Modified 6 months ago Viewed 3k times
How to plot a stacked barchart in phyloseq of relative abundances per ...
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 this Sample …
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 contains all the …
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
r - Trying to generate ASV table from phyloseq - Stack Overflow
Sep 14, 2022 · 0 I think you're looking for the phyloseq::psmelt function, which combines the otu_table, tax_table and sample_data tables into a single, long format table that is suitable for analysis. One …
Phyloseq, how obtain the relative Abundance by merge_samples?
Nov 27, 2019 · I'm trying to obtain the relative abundance using a merge_sample option of the Phyloseq package. When I calculate the average of each Phylum (I will use GlobalPatterns as example) with …
r - Rarefaction curve - Stack Overflow
Jun 24, 2023 · I would like to ask why my rarefaction curve both for the rarefied data and non rarefied doesnt seem ideal. What could be a cause to this? This was the script i used: sam.data_soil_rare < …
r - How to subset (or filter?) taxa in a phyloseq object, within a ...
Feb 19, 2022 · subset <- filter_taxa(phyloseq_object, function (x) sum (x) > 0.35, TRUE) I am having trouble figuring out how to apply this filtration step to see if these taxa belong within >= 70% of my …
Removing spurious taxa from a phyloseq object - take 2
Mar 8, 2023 · Removing spurious taxa from a phyloseq object - take 2 Asked 2 years, 8 months ago Modified 2 years, 8 months ago Viewed 797 times