Tag: phyloseq

How to make alpha diversity boxplot?

How to make alpha diversity boxplot? 1 How to make alpha diversity boxplot? I am trying to perform alpha diversity and I performed scatter plot for shannon measure,How can I make boxplot?? meta.physeq = sample_data(meta) tax <- otu_table(tax,taxa_are_rows=FALSE) physeq.alpha = phyloseq(ASV, tax, meta.physeq) sample_data(physeq.alpha)$shannon.physeq <- estimate_richness(physeq.alpha, measures=”Shannon”) plot_richness(physeq.alpha, measures=”Shannon”) alpha_diversity…

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phyloseq – R: How can I fix an as.matrix() error message?

I am trying to create a taxonomic reference for some 16S/18S data in R and have been running into issues when following this tutorial. I am trying to create an OTU table from a taxonomy/sequence table that was bootstrapped for only 18S data. Here is the error I receive and…

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I cannot install “microbiome”

Hi there, i cannot install package “microbiome” in R (ver 4.2.1), when i input the code, it seems OK, BiocManager::install(“microbiome”, force = TRUE) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) ‘microbiome’ trying URL…

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r – 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 have CYANO_gen <- CYANO %>%…

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How to pool phyloseq data?

How to pool phyloseq data? 0 @688ee615 Last seen 1 day ago United Kingdom I hope someone can help. I am trying to carry out some differential abundance analysis on some microbiome data that has come from a metabarcoding experiment using 16S illumina sequencing. I have processed my data using…

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ggplot2 – Fail to plot by group on a phyloseq object generated by R package Divnet

Once you already have your phyloseq object df_family, you can use the function estimate_richness from phyloseq. You can then join the sample meta data to this data frame of alpha diversities. Finally, you can use ggplot2 directly to customize your plot accordingly, e.g. to put different sample groups (here SampleType)…

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r – RC Bray function not accepting phyloseq otu_table as argument

I am using James Stegen et al’s code here to calculate an abundance-weighted raup-crick value for my 16S dataset. I load in my phyloseq object then extract the otu_table. I then use the otu_table as the spXsite argument in the function raup_crick_abundance(). My otu_table is available as a dput() below…

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Issues removing unwanted taxa from phyloseq object

Hi everyone, I am currently in the process of removing unwanted taxa (Kingdom=”Eukaryota”, Family=”Mitochondria”, and Order=”Chloroplast”) from a phyloseq object I created. This phyloseq object was created using my outputs from DADA2 (OTU table, taxonomy table, and metadata file). I have saved a taxonomy table in CSV format at every…

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r – 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 started…

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Predict Functional potential microbial communities

Predict Functional potential microbial communities – phyloseq Silva 0 Hi, Does anyone have good tutorials/resources on how to predict the metabolic potential from microbiome data. I have preprocessed using DADA2, resulting in a phyloseq object. I assigned taxonomy with SILVA database. I found this Tax4fun package in R implemented in…

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How to order sample names with the phyloseq object for heatmap

Hello!I am new to the Rstudio!I can’t find a tutorial, or instructions for ordering our samples in the heatmapI have created the phyloseq object with the next scripts physeq<-qza_to_phyloseq(features=”file path/rarefied_table.qza”,metadata=”file path/Metadata.tsv”)taxonomy = read.csv(“file path/taxonomy.csv”,sep=”,”,row.names=1)taxonomy =as.matrix(taxonomy)TAX = tax_table(taxonomy)data_full<-merge_phyloseq(physeq,TAX) then I use ph = tax_glom(data_full, taxrank=’Genus’,NArm=FALSE)TOP = names(sort(taxa_sums(ph), TRUE)[1:20])TOPp = prune_taxa(TOP, ph)plot_heatmap(TOPp,…

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Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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

This is to the part of the question “replace actual sequences with OTU ids (Phyloseq/dada2)?” I contacted the phyloseq/dada2 developers and based on Susan Holmes’ reply (github.com/joey711/phyloseq/issues/1030) I came up with this piece of code to replace the amplicon sequences with a numbered OTU header. Further discussion can be found…

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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, ordBC, color = “Stage”, label=”SampleID”) + ggtitle(“PCoA: Bray-Curtis”) graph…

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Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis

1. Eyun, S. Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol. Biol. 17, 23 (2017). PubMed  PubMed Central  Google Scholar  2. Eyun, S. et al. Evolutionary history of chemosensory-related gene families across the Arthropoda. Mol. Biol. Evol. 34, 1838–1862 (2017). CAS  PubMed …

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t-SNE for microbiome analysis

t-SNE for microbiome analysis 1 Hi I wondered whether there is a good tutorial on how to make t-SNE plot on microbiome samples. I have a phyloseq object for which I have metadata age and gender. Ideally I want something like this: So different shapes for gender, and in my…

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Phyloseq Objects for different time points

Phyloseq Objects for different time points 0 Hi I am very new to this microbiome analysis so this might be a very simple question… I have a question related to the microbiome analysis I’m doing. I have microbiome data from 3 different timepoints (T1, T7, and T13), for I made…

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How to get normalized count table from DESeq?

How to get normalized count table from DESeq? 1 Hi, I’m using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all <- DESeq(ds.all,fitType = “local”) Then as the results I got 8 ASVs that showed significantly different….

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Network plot using NetCoMi and igraph

Hi, I am trying to plot the Network plot as suggested here (github.com/stefpeschel/NetCoMi#single-association-network-on-genus-level) by using igraph and NetCoMi. But I am not getting the network plot as expected- I just want to label the hub genera and phyla. and want the network plot in spherical layout. # Agglomerate to genus…

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Bioconductor – DESeq2

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

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export ANCOM-BC normalisation matrix

Hello! I have similar doubt. Did you solve it? I run ancombc with my Phyloseq opbject and extract the data, but we are not certain about the normalization: out = ancombc(phyloseq = phyloseq_obj, formula = “condition_1”, p_adj_method = “BH”, zero_cut = 0.90, lib_cut = 1000, group = NULL, struc_zero =…

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