non-Emperor PCoA in q2

[Tyler_Carrier]

Hi all,

Is there a non-Emperor PCoA option in q2 that is similar to "make_2d_plots.py" in q1? I'm looking for the aesthetic and manipulability (via other programs) that can be performed on the "make_2d_plots.py" output.

Regards,
Tyler

[Nicholas_Bokulich]

Hi @Tyler_Carrier,

@Tyler_Carrier

Is there a non-Emperor PCoA option in q2 that is similar to “make_2d_plots.py” in q1?

emperor does have a 2d plot option (I believe it is in the axis tab, just set the 3rd axis to "none"). Right now there is nothing else in q2 that can give you a q1-like pcoa plot.

@Tyler_Carrier

I’m looking for the aesthetic and manipulability (via other programs)

Two options, both pretty easy. Export your pcoa coordinates artifact and:

1. use qiime 1 if you like that aesthetic
2. plot in R (e.g., with phyloseq)

[Tyler_Carrier]

Hi Nicholas,

What file should be used in Qiime1 to make 2D PCoA?

Regards,
Tyler

[Nicholas_Bokulich]

The pcoa coordinates artifact (i.e., the same input you use for emperor). But you must export that artifact to use it with q1, R, or any other program.

[Tyler_Carrier]

Hi Nicholas,

I've done the following:

qiime diversity beta-phylogenetic
--i-table Table "post-pair, QC, deblur, rare".qza
--i-phylogeny tree_rooted.qza
--p-metric unweighted_unifrac
--p-variance-adjusted
--o-distance-matrix unwUniFrac_distmatrix.qza

qiime diversity pcoa
--i-distance-matrix unwUniFrac_distmatrix.qza
--p-number-of-dimensions 2
--o-pcoa unweighted_unifrac_PCoA.qza

qiime tools export
--input-path unweighted_unifrac_PCoA.qza
--output-path unweighted_unifrac_PCoA_forQ1

#in qiime1
make_2d_plots.py
-i unweighted_unifrac_PCoA_forQ1/ordination.txt
-o unweighted_unifrac_PCoA_forQ1_2Dplot
-m Lv_DiffFeeding_q2_metadata.txt
-b 'Variable'
--ellipsoid_opacity 0
--scree

This results in "IndexError: index 2 is out of bounds for axis 1 with size 2"

Is there is way around this?/Am I using the correct file for q1?

Regards,
Tyler

[Nicholas_Bokulich]

Hi @Tyler_Carrier,

@Tyler_Carrier

This results in “IndexError: index 2 is out of bounds for axis 1 with size 2”

Sorry, we cannot provide support for QIIME 1 on this forum.

The format of your coordinates file may be incorrect... here's an idea: instead of exporting as you are, use qiime metadata tabulate --m-metadata-file unweighted_unifrac_PCoA.qza --o-visualization unweighted_unifrac_PCoA.qzv, then view that output and download as a CSV. Try using that as input to the qiime 1 command.