Getting more than two axes with `ordinate`

[lvclark]

I'm doing NMDS with ordinate and trying to get three axes rather than two. I see in the documentation that I can set k = 3. This works with the Bray distance, but not with UniFrac or weighted UniFrac. It seems to be an issue with argument handling.

Error in UniFrac(physeq, ...) : unused argument (k = 3)

[lvclark]

I was able to work around this by calling phyloseq::distance followed by vegan::metaMDS.

[elenu]

Hi @Ivclark,

I had similar issue, and I managed by running this way and visualizing with scatterplot3d package. Maybe, you could adapt it to your case:

library("scatterplot3d") # load
nmds <- ordinate(physeq3, "NMDS", "bray", "unifrac", weighted=TRUE)
s3d <- scatterplot3d(nmds$species, angle = 55,type="h", 
                     main="3D NMDS",
                     xlab = "NMDS-1",
                     ylab = "NMDS-2",
                     zlab = "NMDS-3", pch = 16,size=6, 
                     grid=TRUE, box=FALSE)
s3d
text(s3d$xyz.convert(pcoa$species), labels = rownames(nmds$points),
     cex= 0.7)

[TonyMane]

greetings @lvclark, i'm a bit new to phyloseq, was wondering if you could describe the code/function you developed to get a 3-ordination and subsequent plot out for phyloseq.

[lvclark]

Hi @TonyMane in this particular case I did

dist_unifrac <- phyloseq::distance(ps_prop, "unifrac")
nmds_unifrac <- vegan::metaMDS(dist_unifrac, k = 3)

See https://github.com/HPCBio/plotly_microbiome, a package I made for making 3D plots from the output. Install then do ?beta_diversity_3d.

[TonyMane]

thanks, much appreciated. One question, it doesn't seem to handle the output of nmds_unifrac from above: beta_diversity_3d(nmds_unifrac) Error in data.frame(x$points[, 1:3], metadata[, color.column], Label = rownames(x$points)) : argument "metadata" is missing, with no default

[lvclark]

Please see the help page. In that case you would be using the method for monoMDS and so you need to provide values for the metadata and color.column arguments.

[TonyMane]

greetings, was just wondering if there was any way to plot these directly to a pdf file. I run all the commands and get the 'index.html' files to plot, then export as a .png file. But it would be ideal to have .pdf files.

[lvclark]

@TonyMane See if this helps https://plotly.com/r/static-image-export/

[RachBioHaz]

Hi @TonyMane in this particular case I did

dist_unifrac <- phyloseq::distance(ps_prop, "unifrac")
nmds_unifrac <- vegan::metaMDS(dist_unifrac, k = 3)

See https://github.com/HPCBio/plotly_microbiome, a package I made for making 3D plots from the output. Install then do ?beta_diversity_3d.

Hi, I'm a new user of plotly_microbome and new(ish) to bioinformatics. Can I suggest the help page contains information on the data structure of your examples? Thanks

[lvclark]

@RachBioHaz I made that package mostly for internal use at an old job, so I'm not maintaining it any more. But ps_prop would be a phyloseq object with abundances converted to proportions.