Beta diversity inconsistent results between 2D and 3D plot

I have been performing beta diversity analysis in microbiomeanalyst for several biomarkers using PERMANOVA. I noticed that, in the 3D plot, the marker labels are switched (ie showing the opposite results from the 2D plot). I have pasted an example below as well as the R code. This is the same for 4 different markers I have tried. I wonder if there is an error in the code that is causing the labels to be switched between the two plots?

1. mbSet<-Init.mbSetObj()
2. mbSet<-SetModuleType(mbSet, “mdp”)
3. mbSet<-ReadSampleTable(mbSet, “emma-meta.csv”);
4. mbSet<-Read16STaxaTable(mbSet, “LTBE.csv”);
5. mbSet<-Read16SAbundData(mbSet, “EmmaOTUfinal.csv”,“text”,“SILVA”,“T”,“false”);
6. mbSet<-SanityCheckData(mbSet, “text”);
7. mbSet<-SanityCheckSampleData(mbSet);
8. mbSet<-SetMetaAttributes(mbSet, “1”)
9. mbSet<-PlotLibSizeView(mbSet, “norm_libsizes_0”,“png”);
10. mbSet<-CreatePhyloseqObj(mbSet, “text”,“SILVA”,“F” , “false”)
11. mbSet<-ApplyAbundanceFilter(mbSet, “prevalence”, 0, 0.1);
12. mbSet<-ApplyVarianceFilter(mbSet, “iqr”, 0.0);
13. mbSet<-PerformNormalization(mbSet, “none”, “none”, “none”, “true”);
14. mbSet<-PerformBetaDiversity(mbSet, “beta_diver_0”,“PCoA”,“bray”,“expfac”,“PR3_HIGH_LOW”,“none”,“OTU”,“”,“Chao1”, “yes”, “adonis”, “png”, 72, “default”);
15. mbSet<-PCoA3D.Anal(mbSet, “PCoA”,“bray”,“OTU”,“expfac”,“PR3_HIGH_LOW”,“”,“Chao1”,“beta_diver3d_0.json”)
16. mbSet<-PerformCategoryComp(mbSet, “OTU”, “adonis”,“bray”,“PR3_HIGH_LOW”);


Thanks for letting us know about the bug, the issue should be fixed now. Can you check with your data whether it works with your data?


please , 3d plot for beta diversity appear like this although i used it before several times, how can i solve this problem?

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