I'm facing a problem with the PCoA plots of my non-phylogenetic core metrics analyses with ITS amplicon data. I aim to compare two groups (healthy and patient samples) but for any reason I'm only seen 8 instead of the 12 patient samples.
jaccard_emperor.qzv (950.5 KB)
bray_curtis_emperor.qzv (950.6 KB)
(look for "Collective")
It looks like that these 4 samples are displayed together at the same position in the 3D space.
I have a look to the distance matrix and distances of these samples to all others showed 1.
distance-matrix.tsv (7.4 KB)
I have a look to the feature table and and absolute counts obtained from the taxabarplots and I had a lot of features with 0 in a lot samples, so I tried to filter out low abundance features. After trying a lot of parameters I think I found the best for my dataset with following command:
qiime feature-table filter-features-conditionally --i-table table_H_E0_NL.qza --p-abundance 0.01 --p-prevalence 0.03 --o-filtered-table table_H_E0_NL_pa0.01_pre0.03.qza
I was able to get rid a lot of features (from 949 to 288) where sampling depth was still quite ok (from 1425 to 1405).
no filter data:
table_H_E0_NL.qzv (566.3 KB)
barplots_H_E0_NL_UNITE2022_single.qzv (489.1 KB)
table_H_E0_NL_pa0.01_pre0.03.qzv (542.5 KB)
barplots_H_E0_NL_UNITE2022_single_pa0.01_pre0.03.qzv (465.2 KB)
Taxonomy composition, in term of diversity, differs a lot between the groups.
Once I performed the core_metrics I just only gained one sample on the plot, 3 others were still at the same position in this spatial space.
jaccard_emperor.qzv (956.0 KB)
distance-matrix.tsv (7.3 KB)
I thought that maybe the metric is not the right choice, so I found this nice post Alpha and Beta Diversity Explanations and Commands and give a try to a bunch of metrics and in only one "roger" the 12 patients samples were seen on the plot. Nevertheless, I don't like the distribution of the samples that much.
roger_plot_E0_HNL_NL.qzv (948.2 KB)
I used forward reads only for these analyses and followed DADA2 strategy for denoise.
I don't know how to proceed and maybe you have any idea? I will really appreciate any suggestions
(Sorry for the long post!)