I'm new to QIIME2. I'm trying to make a PCoA plot in both QIIME2 and R. I have some questions regarding the dimensions of pcoa plots.
Take the Jaccard distance matrix of beta diversity as an example.
In QIIME2, I run
qiime diversity core-metrics and got the
jaccard_pcoa_results.qza for pcoa results. When I opened this file using R and found that it has PC155, which means QIIME2 generated 155 dimensions. When I viewed the
jaccard_emperor.qzv through QIIME2 view, the default number of the axis was 3.
Then I wanted to use
jaccard_pcoa_results.qza (the one that has 155 dimensions/axes) and make a PCoA plot that only has two dimensions/axes using ggplot in R. Can I still use
jaccard_pcoa_results.qza file to do so as I can just choose to use PC1 and PC2?
Because this looks suspicious to me, I ran these commands in QIIME2 to make sure that my PCoA file only has 2 dimensions:
(qiime2-2023.5) busihan@SihandeMacBook-Pro Rerun_3rd_final % qiime diversity pcoa \ --i-distance-matrix core-metrics-results-decontam-genus/jaccard_distance_matrix.qza \ --p-number-of-dimensions 2 \ --o-pcoa core-metrics-results-decontam-genus/jaccard_pcoa_2_dimensions.qza Saved PCoAResults to: core-metrics-results-decontam-genus/jaccard_pcoa_2_dimensions.qza
(qiime2-2023.5) busihan@SihandeMacBook-Pro Rerun_3rd_final % qiime emperor plot --i-pcoa core-metrics-results-decontam-genus/jaccard_pcoa_2_dimensions.qza --m-metadata-file Mapping_File.tsv --o-visualization core-metrics-results-decontam-genus/jaccard_emperor_2_dimensions_plot.qzv Saved Visualization to: core-metrics-results-decontam-genus/jaccard_emperor_2_dimensions_plot.qzv
It turned out that my
jaccard_emperor.qzv (the one that has 155 dimensions in PCoA file) and
jaccard_emperor_2_dimensions_plot.qzv(the one that has only 2 dimensions in PCoA file) look very different through QIIME2 view, even though I chose to present only 2 axes in
jaccard_emperor.qzv. Could you please explain this to me?
Thank you for your help!!