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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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1 answer

combine OTU and tax table and replace actual sequences with OTU ids (Phyloseq/dada2)

I was following the workflow described here https://f1000research.com/articles/5-1492/v2 using the sample data as well as my own data. This worked fine, but now I can't generate an OTU table, that contains a header such as "OTU00004" or even better…
crazysantaclaus
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3
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1 answer

R calculate most abundant taxa using phyloseq object

I would like to know if my approach to calculate the average of the relative abundance of any taxon is correct !!! If I want to know if, to calculate the relative abundance (percent) of each family (or any Taxon) in a phyloseq object (GlobalPattern)…
abraham
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3
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3 answers

How to creat a bar graph of microbiota data with one color for higher taxonomic rank and gradient color

I have a Phyloseq object with my OTU table and TAX table. I would like to create a bar plot, at for instance family level, but families belonging to the same Phylum will be displayed with the same colour and be distinguished by a gradient of this…
Thibault
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1 answer

efficient subsetting in R phyloseq ignoring missing parameters

I'm using phyloseq a lot for my work. My data sets often contain multiple conditions or parameters, which need to be analyzed in the same way (for example the same plot for Bacteria in Summer or Winter AND in Lake1 or Lake2), so I wanted to use…
crazysantaclaus
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3
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1 answer

ggplot2 object in Phyloseq - how to reorder the x axis entries?

mapfile = "map_soil_final3.txt" map = import_qiime_sample_data(mapfile) print(map) tree = read_tree("rep_set.tre") biom = "otu_table_15000_json.biom" biomfile = import_biom(biom,parseFunction=parse_taxonomy_default) testdata =…
user3105519
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3
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1 answer

Phyloseq ggplot2 objects do not allow certain elements to be added

I would like to modify plots produced by the phyloseq package (download it from github). Phyloseq plots are ggplot2 objects, so I would think that I could add elements by adding ggplot2 objects to to the phyloseq-created object. In some cases this…
K. Brannen
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1 answer

Change size of label annotations in a ggplot

I am trying to change text label sizes inside my plot (not the axes, rather the label annotations) I am working with a phyloseq object but I don't think that matters. Here is the code and the output. Any suggestions? plot_ordination(prokaryote_ra,…
Ezra Orlofsky
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2 answers

error while writing file after adonis analysis

I am trying to write output from permutation analysis by using below code but it shows error, could you please suggest how I can resolve this error? R code ###adonis_calculation BC <- phyloseq::distance(phyloseq_prop, "bray") pmv =adonis(BC…
bioinfonext
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1 answer

Why is R unable to access index for repository of bioconductor

When trying to install bioconductor (for installing phyloseq package) I get several warning and error messages I got a new harddrive few days ago so I had to reinstall all programs including R with all the packages I usally need. Everything worked…
Barbs
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0 answers

How to fix "Each row of output must be identified by a unique combination of keys" error in R

I'm new to R. I have uBiome data (in csv) that I want to convert to Phyloseq. Been trying to use this R package called Actino, but whenever I use the actino::experiment_to_phyloseq() function, "Error: Each row of output must be identified by a…
Marie Francisco
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1 answer

filter phyloseq to use in fantaxtic

I want to make a barplot using the library fantaxtic (top taxa: Phylum and nested taxa Genus). The problem is that I want to filter Genus by abundance > 2% and the rest of phyla I want to group them in the category Others. Is it posible? Can library…
user1892205
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0 answers

RStudio plot window won't finish loading and/or won't properly load my plot

I'm trying to create a plot showing the abundance of ASVs within control vs true samples. This isn't an issue with the code since I've used it before and it was just working yesterday, but I'll include it here: # Starting from a phyloseq object…
Katie
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0 answers

Merge two phyloseq with different taxonomic data

I have 7 samples, I can successfully create a phyloseq file, make a distance matrix and calculate the beta diversity with adonis2. However, I want to add one more sample from an earlier sequencing, so I have to work with a different shared, taxonomy…
vicey
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1 answer

I can't get the coefficients of the taxa that contribute to the groups differences

I'm trying to get the coefficients of the taxa that generate the most differences between the groups in my permutest of types of supplies for the animals. I paste the results of the permutest: permutest(betadispersionAlimentación, pairwise =…
Srvcl
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1 answer

error vegan rarecurve Error in as(x, "matrix")[i, j, drop = FALSE] : (subscript) logical subscript too long

I am trying to plot some rarefaction curves, but I am getting this error: Error in as(x, "matrix")[i, j, drop = FALSE] : (subscript) logical subscript too long I am giving a reproducible example on how I use the function: …
i.b
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