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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

141 questions
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tax_glom() or merge_samples() inhibits downstream calls for sam_table() categories

I have data with OTUs representing fungal taxa I have discovered through metabarcoding of moths with ITS2 primers. I have a phyloseq object with an otu_table, tax_table, and sam_data. In sam_data I have categories with all taxonomic levels of the…
sondre
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After separating into columns, how do I sort my data so that it's in the right column?

I have a taxonomy list created from bracken that I want to import to phyloseq. I have my taxa in one column like…
sisherb
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phyloCorrelogram() issues

I've been struggling with phyCorrelogram() from the package phylobase. I have received a myriad of errors this past month, and I have come full circle with the first error again. (yay) I am enormously grateful for any help. The phyloseq object…
Geomicro
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Failure to install phylosmith - unable to load shared object, undefined symbol

Setup: R version 4.0.5 (2021-03-31) -- "Shake and Throw" Platform: x86_64-pc-linux-gnu (64-bit) Ubuntu 16.04 Issue: Cannot install phylosmith package. Command: devtools::install_github('schuyler-smith/phylosmith', lib =…
BeefWellington
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Transformation introduced infinite values in continuous y-axis

I want to set my y-axis to log-scale to make the visualization better readable. Before doing so my data looks correctly displayed . without log-scale plot_bar(ent40, "phylum", fill="kingdom", facet_grid=~sampleID)+ geom_col(aes(fill=kingdom),…
mr.raccoon
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Get tree from ancestor nodes of cutree groups R

I have a tree and I want to get part of the tree that is ancestors of cutree groups. library(stats) library(ape) tree <- ape::read.tree(text =…
Shubham Gupta
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Warning message: Setting row names on a tibble is deprecated

I encountered this warning message while changing the row names: Warning message: Setting row names on a tibble is deprecated. Can anyone please help me to this warning message/error? Thanks and regards, DC7
CHANDA7
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generating out_table in R

How can I neatly and easy generate an out_table. I classified groups with cutree() of a hclust() object. My samples are diet protocols. In my otu_table, the diets shouöd be the samples and the taxa should be the groups. example #base data for the…
takeITeasy
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How to deal with quotes around an argument in a function?

I have a function I am trying to make in R that looks like this: diff_abund <- function(Data, Rank, Taxa) { subset_taxa(Data, Rank == Taxa) } da= diff_abund(frbc1_02, Phylum, "Acidobacteria") And I get the error: Error in eval(e, x,…
Sam Degregori
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Phyloseq, how obtain the relative Abundance by merge_samples?

I'm trying to obtain the relative abundance using a merge_sample option of the Phyloseq package. When I calculate the average of each Phylum (I will use GlobalPatterns as example) with all the samples; I mean, Globalpaters have 26 samples so I made…
abraham
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Converting existing data in R into Phyloseq OTU table

I have been attempting to "phyloseq-ize" my asv_table, asv_id, and metadata for a 16S analysis, created using qiime2 and uploaded to R using read.table(). I have been able to successfully import my asv_id and metadata (using tax_table() and…
Geomicro
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get structure of unrooted tree with tree_layout()

Is there a way to get the structure of an unrooted tree with the phyloseq::tree_layout() function? Using tree_layout() will give you the coordinates of the nodes and segments that compose the tree plotted below. You can then easily redraw that…
Sebastien Renaut
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How to add species arrows/vectors to an ordination plot

I have made ordination plots of microbiome data using the R phyloseq functions ordinate and plot_ordination with a phyloseq object and a previously calculated distance matrix (unweighted UniFrac distances) as inputs. I would like to add some arrows…
eok
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How do I use the NULL Value as a variable call in R Shiny

How do I pass NULL as a Variable Value in RSHINY? In phyloseq, there is a plot called plot_net. The most basic plot_net plot code looks like this: data(enterotype) #Eliminate samples with no entereotype denomination enterotype =…
Ariel A
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How to remove very thin Bar Plot outline/border

I wanted to remove these lines at the edge of my bar plot. I am using the phyloseq library. Here is my code, I tried changing colour/color/col to "NA" and it is the same result. I just don't like that little thin black outline.…
Mohammed Rahman
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