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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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Looking for code in R to summarize by ____H or ____D?

I have a chart with ASV's per sample, the samples are sorted by number (sample) and a letter which corresponds to human or dog. I am trying to see which ASV's are in only humans, or only dogs. My thought for how to do this is sum all rows by dog or…
Isabella Raux
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Trying to subset a large table using counts of all row values in a single column

Working in R on genomic data. I'm trying to subset a very large melted phyloseq table, which includes a column of phylum IDs, in order to remove rows containing phyla that occur less than 100000 times in the table. I might have missed an "easy" way…
carrollk2015
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Compute and plot bootstrap values with ggtree

I have a file with the phylogenetic tree that is the output of doing RAxML. I want to plot this tree with the R package ggtree and show the bootstrap values and the internal numbers of the nodes. The actual code plots the tree with the node numbers,…
Marta N
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Normalization method

I am a PhD student working on microbiome 16S rRNA sequence data. I have this code for phyloseq normalization from a previous student and wanted to ask if someone could help explain exactly what it is doing: ps_norm <- transform_sample_counts(ps,…
MAlvarez
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Order x-axis categorical variable using another categorical variable

I have a dataframe like follows: Class ID Stage Abundance Substrat OTUA rep1 A-X1 123 G OTUA rep2 A-X1 234 PC OTUA rep3 A-X1 [numerical values] [only two categorical…
Laurence Auger
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How do I generate scatterplots for abundance and a numerical variable with a phyloseq object?

I have a phyloseq object in R, and I would like to generate scatterplots to show associations between individual taxa and a numeric variable that's in my sample data (i.e. my variable on x axis, abundance of particular taxa on y axis). I guess I…
Kate
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Calculate top taxa per sample in a phyloseq object

I need to calculate the top 6 taxa in each individual sample of my phyloseq object. It seems like it should be a simple request...but I have not been able to find a way to do this! Thank you
MAlvarez
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Stacked bar chart with OTUs identified to different taxonomic levels

I have microbiome data with OTUs identified to the lowest taxonomic level possible. Some of the OTUs are identified to genus, others to family, order, etc. I need to create a stacked bar chart. My problem: If I choose "genus" for my bar chart,…
MAlvarez
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phyloseq: Discrepancies in otu counts before and after using tax_glom

Maybe I missed something in how tax_glom works but as I did not find any info here nor elsewhere on the web, maybe someone here can help. I do not provide data but I can on request. Here is the code highlighting the issue I…
GTC
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Fail to plot by group on a phyloseq object generated by R package Divnet

I intend to plot an alpha diversity plot of my samples, which consist of three groups. Alpha diversity is calculated by R package Divnet. It involve using phyloseq as a dependency. The group of each sample is specified in a sam_data, column "type"…
ivanllam
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How to subset (or filter?) taxa in a phyloseq object, within a grouping?

I am attempting to subset (or filter?) taxa that have relative abundance >= 35%,and belong in >= 70% of samples within a grouping (in my case it is the number of 'clusters' in my data). Is there a simple line of code on how to do this? I have…
Dominika Boron
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How to attach metadata to a phylo4d tree

I am working to attach metadata to a phylo4d tree. I will start by saying I can attach my objects as a dropbox file, but if I am just misunderstanding the logic I'll save myself and everyone's time. I start with a phyloseq object then extract the…
Geomicro
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Trying to change colour of one variable in ggplot geom_bar dependent on the string

I have a for loop to run through a tonne of microbiome data (using phyloseq) and generate plots for multiple experiments. ggplot(data_M1, aes(x = Sample, y = Abundance, fill = get(i))) + geom_bar(stat = "identity")+ facet_wrap(vars(Status,…
DS14
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Phylo tree has no branch lengths using phylosig () R

I am having a hard time understanding why my phylo tree (imported as a phyloseq object from QIIME2) appears to have no branch lengths when used in phylosig(). I am trying to compute the phylogenetic signal of my 16S dataset compared to a single…
Geomicro
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Editing tables with R studio

Phylum Abundance Bacteroidetes 12 Firmicutes 4 Proteobacteria 3 Firmicutes 21 Firmicutes 9 Bacteroidetes 15 Proteobacteria 3 Bacteroidetes 8 Verrucomicrobia 2 Bacteroidetes 5 My question is I have a table like above in…
Mücahit Kaya
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