Is it available to Make 2D PCoA Plots?

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1

Dear Qiime2 masters,
I am wondering if we can make 2D PCoA Plots instead of 3D plots in Qiime2.
If not, could we export a certain file and make the 2D plot in Qiime1?
Thanks!

Ganyu

3

Hi @agan!

QIIME 2 does not currently support 2D PCoA plots. There's an open feature request and pull request on the Emperor GitHub repository to add this feature. QIIME 2 wraps Emperor to produce PCoA plots (via the q2-emperor plugin), so when Emperor has 2D plotting functionality q2-emperor will be updated to support it as well.

Yep! You can export the ordination coordinates file from your .qza file and supply it to QIIME 1's make_2d_plots.py. For example, using the unweighted UniFrac ordination results and sample metadata in the QIIME 2 Moving Pictures tutorial:

qiime tools export --output-dir exported unweighted_unifrac_pcoa_results.qza
make_2d_plots.py -i exported/ordination.txt -m sample-metadata.tsv -o 2D-plots
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5

Thanks a lot for your help, Jai!

Ganyu

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6

Hello @agan,

As @jairideout mentioned, this functionality is in the pipeline, but has not made it in yet, my estimate is that we will be able to have two dimensional plots by the end of August. These will be provided interactively as part of the current GUI.

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7

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9

2D PCoA is now supported in the latest release (2017.9)! Thanks to @yoshiki for the functionality!

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