create a PCOA plot using emperor tool

Dear all,

I used the following command line after performing beta diversity analysis to generate PCOA plot :
qiime emperor plot
–i-pcoa unweighted_unifrac_results.qza
–m-metadata-file sample-metadata.tsv
–o-visualization file.qzv
i obtained the following error message :
Invalid value for “–i-pcoa”: Expected an artifact of at least type PCoAResults. An artifact of type DistanceMatrix was provided.

What is the command line that i can use to generate pcoa results.qza in order to use this last file as input to generate PCOA plot using emperor tool ?

Thanks

Hi @M_F,
See this section of the overview tutorial for a flowchart describing the steps involved in generating emperor plots (individually vs. using the core-metrics pipelines).

As the error message describes, you input the wrong data type.

First you need to perform PCoA:

qiime diversity pcoa

Then visualize these PCoA results with emperor:
qiime emperor plot

Good luck!

1 Like

Hello
@Nicholas_Bokulich

Thanks you so much. I obtained a pcoa plot with a background color black i didn’t find an option to convert it to white. Is there any option to change the background color ?

i think also that there is no option to save the image as TIFF
Thanks for you help

Hi @M_F!

Yes! Check out this screenshot:

You can pick a new “Background color” using the dropdown on the right side of the screen:

You can save as a PNG, which is a lossless format:

If you need a TIFF, you will need to use another software package to convert the PNG to TIFF.

Hope that helps!

:qiime2:

2 Likes

Hello
@thermokarst thanks a lot

1 Like