hello ... I was wondering if there is a plug-in you provide to calculate the percent of each of the relative abundance taxa from the total abundance?
as you can kindly see I created that the ones below 1% in abundance but I need to create or produce a table which contains how each taxa constitutes of the total abundance
Also, would be helpful if you suggest a way to use outside if not available in qiime2
as I found in papers that they mention the percent for each taxa in groups of samples
Hello!
You can obtain relative abundances of the taxa from absolute counts.
Qiime2 solution.
Collapse your table to desired taxonomy level
Convert it to relative abundances.
You can find corresponding plugins in Qiime2 docs.
You also can do it outside of the Qiime2 environment.
Download a csv file from taxabarplot visualization at desired rank, and divide the count of each taxa in a sample by the sum of all taxa counts within given sample. To get percentage, multiply it by 100.
Note that if you will filter some taxa from the table before this step, it will affect relative abundances of remaining taxa.
But how then to report it if it is for each sample? can't make for a group?
In papers I can see this sort of reporting:
At FW1, ASV8, a Firmicutes from the family Ruminococcaceae , made up 17.9% and was also the most abundant ASV at FW2. ASV20 (Lactobacillus sp. ) was the most abundant ASV at FW3 (5.9%) and FW4 (8.5%). At 1-week post-SWT (SW1), a single Proteobacteria of the genus Vibrio (ASV5) made up 19.4% of abundance, and after 4 weeks in SW (SW2), ASV7 (Vibrio sp. ) constituted 24.9% of total relative abundance.
Do they take the average percentage of the samples in a certain group?
I would be grateful if you could advise on this?
M
Hello!
Just for sanity check, now it is a good idea to check if there is no errors in the relative abundance calculation - do all taxa in a given sample summed to 100%?
Yes, I guess they took an average by groups.
To reproduce:
Option 1. Add group information to your table and average the entire table by groups (note that if you will group absolute abundances and then transform it to relative ones can give you slightly different results than if you will group relative abundances).
Option 2. Group your feature table by groups in Qiime2, than convert it to relative abundances, export your table as a tsv.
