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[Multi Dimensional Scaling](https://en.wikipedia.org/wiki/Multidimensional_scaling) (MDS) and Principal Coordinate Analysis (PCoA) are two names for the same dimension reduction technique*.
In [sci…
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Hi
Could you please clarify if you transform your samples before plotting PCA/PCoA?
Thanks
Marwa
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Dear Joey,
I am trying to make some ordination plots on my data, but I always encounter errors when I use `type = "samples"` using plot_ordination.
`> mydata`
`phyloseq-class experiment-level object…
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il faudrait qu'on soit bien calés sur les 2 premiers axes de la PCOA en termes d'interprétation. Qu'en dis-tu Olivier?
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- **LDA**
- Remove `--input_data_type` parameter.
- utilize argparse checks for relevant input files for bubble plots.
- Consolidate figure sizes for LDA and LDA bubble plots.
- Add optional…
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Hello!
First of all, this is an awesome package, and thank you so much!
I constructed 6 ordination plots with my data, and I am trying to collect them together. However, although I have tried mu…
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First, thanks for this extremely useful package and detailed explanations on tree metrics and visualizations in treespace as well as assessments of those visualizations.
I have a question about the…
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I was taking a look through the source to reconcile some discrepancies in how I was computing explained variance in my own code for PCoA. I noticed that around line 99 of `_principle_coordinate_analys…
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Greetings,
I am working on a microbiomes project and did an principal coordinates analysis in Phyloseq with the following script:
ordu = ordinate(qd.red, "PCoA", "unifrac", weighted = TRUE)
p = pl…
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Hello, I am working with COI metabarcoding data of 24 samples, and there are many zeroes in the data frame, as some zotus are not detected in certain samples. I am using the `transform_sample_counts` …