Hello,

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?

I attached my files here:

jaccard_emperor_2_dimensions_plot.qzv (963.1 KB)

jaccard_emperor.qzv (968.1 KB)

jaccard_pcoa_results.qza (415.4 KB)

jaccard_pcoa_2_dimensions.qza (184.1 KB)

Thank you for your help!!