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Questions tagged [phyloseq]

phyloseq is an R package with functions and tools to handle and analyze high-throughput microbiome census data

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Errors with tree construct by [ape]

I am trying to plot an MSA tree for my nucleotide sequences. I used toparslan's script. It worked on other files but with the current file, it won't work. Error on distance information? How do I fix this? > [1] "DNAbin" dnbin<-dist.dna(nbin, model =…
Marla Stephany Daniel Toledo
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Rename values in a list based on a dataframe

I am using the function "ps_venn" to compare taxa present in different samples with a phyloseq object. This function outputs a nested list of each sample(s) and the intersecting taxa: Because this is metabarcoding data, the taxa have these long…
Ashley
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plot_ordination function of phyloseq plots shapes 'double' within itself

I'm analysing NGS data using the phyloseq package. I want to create a PCoA (Bray-curtis DM) plot using following code: ord_bc_pcoa<-ordinate(physeq,method="PCoA", distance="bray") pcoa_plot_1<-plot_ordination(physeq,ord_bc_pcoa,color="variable1",…
Robvh
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Using weights in downstream microbiome analysis

I am working on microbiome analysis. I have a metadata containing weights for each participants, which means every participant may represent different number of participants. The weights could help better balance the covariants between comparison…
Zoe Wang
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ntaxa for phyloseq - remove ASVs that sum to 0

I have subset a large phyloseq object from 2000 to only 29 samples. When I put in ntaxa for the new phyloseq object, it gives me >4000 taxa, which is the number from my original phyloseq. How do I remove ASVs that are not present in the new object…
MAlvarez
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Trouble with the nmds_phyloseq function of the phylosmith package: Error in `stat_ellipse()

I am using the phylosmith package to make ordination plots from my phyloseq file (microbial ecology data). Here's the command: nmds_phyloseq(pseq, c("Description"), circle = TRUE, verbose = FALSE) I get the error: Error in stat_ellipse(): ! Problem…
Sweethunderstorm
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circular cladogram showing relative abundance and annotated by factor using phyloseq input

I would like to make a circular cladogram but only showing the changes in relative abundances between factors, as I don't have the phylogenetic tree my phyloseq object only contains otu table, and taxonomy table. I would like to get something like…
i.b
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Issue reinstalling package Phyloseq after updating R to v4.3.0: "fatal error: zstd.h: No such file or directory"

I just installed new Ubuntu updates, and apparently it contained a new version of R (4.3.0), which I didn't realize. I ended up having to reinstall some packages, but there is one that I am having issues, which is 'Phyloseq'. This is the error…
matheusb
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Fantaxtic plot - how do I change the order of my chronological and numerical data?

I am creating graphs with Fantaxtic for phyloseq. I am creating graphs from the same data in two ways. Grouping samples by month: I need to display the months in chronological order, not alphabetical. I tried to set the orders of the months as such…
MAlvarez
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in phyloseq why am I having non-numeric matrix provided as OTU table?

I am trying to run phyloseq and I get the follwing error message OTU = otu_table(otumat, taxa_are_rows=TRUE) Error in validObject(.Object) : invalid class “otu_table” object: Non-numeric matrix provided as OTU table. Abundance is expected to be…
PAR
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How to format NMDS output and betadisperser output to HTML in Rmarkdown

I want to format the output to proper looking tables in rmarkdown with HTML as output. I've having trouble formatting the output objects that result from ordinate function nmds.bray <- ordinate(entero, method="NMDS", distance="bray") and…
Geosphere
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Error In phyloseq alpha-diversity plot - getting a dimensions warning

using plot_richness and sample data myData is a phyloseq data set with 5 taxa from six samples I tried removing and adding variable and nothing gets rid of the error message.
Aerin R-N
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How to take random samples from a Phyloseq object

I have a Phyloseq object like the following: My goal is to take a random sample of size n from this object. Even after trying all sampling functions from the Phyloseq package, I am still unable to complete this task. I would have tried other…
Detr4
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Estimate_richness for all phyla in phyloseq

Is there an easy way to get ASV richness for each Phylum for each Station using the estimate_richness function in phyloseq? Or is there another simple way of extracting the abundance data for each taxonomic rank and calculating richness that way? So…
DiveDaniela
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How to subset a phyloseq object to perform ancombc in R?

I am trying to follow ANCOMBC tutorial at https://bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC.html However I got stacked in the beginning, since I was not able to subset the atlas file. The code is the…
Mani
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