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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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Adonis result does not match the NMDS plot?

I'm not a statistician and kinda working through this blindly, but why does my NMDS plot of bray-curtis measures show clear groupings for status (blue and pink) but adonis says that time point is significantly different? distance_calc <-…
DS14
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A problem with making phyloseq object - Found more than one class "phylo" in cache

I`m trying to make a phyloseq object in R this is my script: Phyloseqb<- qza_to_phyloseq( metadata = "E:/pesticide 4 months work result/pesticide bacteria/pesticidebacteria/metadata1.txt", features= "E:/pesticide 4 months work result/pesticide…
Amani sliti
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change order of x-axis in ggplot2 in shiny app

I have a shiny app created that plots metagenome data using ggplot2, phyloseq, and plotly with dplyr and tidyr. It creates pretty good stacked barplots and heatmaps. The only issue is that it reorders sample names on the x-axis, for example. 1–10…
Ahmedtrio
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Trouble making an object in phyloseq

I'm trying to make an object that I can use in the package phyloseq, but I can't seem to get it to work. Below is a small subset of my data. First is an otu table, the second has the taxa. OTUs <- dput(OTU_table[1:5,]) structure(list(OTU_ID =…
Moriah
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problem in reordering the graph axis ggplot2, phyloseq

i have a shiny appp created which plots metagenome data using ggplot2, phyloseq and plotly with dplyr and tidyr. It creates pretty good stacked barplots and heatmaps only problem is it reorders sample names at x-axis e.g. 1-10 are arranged as…
Ahmedtrio
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Conflicts within function calls to variables in R

I'm somewhat confused with the different values a variable can take within a function and how it is possible to harmonize them so that they suit the different tasks and function calls within the custom function. Here I wrote an example where the…
Lisa
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Having trouble performing mantel test with assymetrical matrices

I am trying to compare distances matrices belonging to two species matrices. One is bacteria and the other is ectomycorrhizal fungi. Both species matrices were generated from the same plant roots using different extraction methods. I want to compare…
srs1085
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sam_data gets transformed into NAs and numerical values when using merge_samples phyloseq

I have sam_data looking like this I want to use the merge_samples() command on the "genus". I have tried with code looking like this: merge_physeq <- merge_samples(physeq, "genus") What happens now is I get several of the warnings: In…
sondre
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envfit nmds error Error in prod(np) : invalid 'type' (list) of argument

I am trying to run an NMDS using as input the abundances of phyloseq object: ps_abu<-microbiome::transform( psxxx, "hellinger") %>% abundances()%>% t() set.seed(123) nmds = metaMDS(ps_abu, distance = "bray", trymax=1) however when I try to…
i.b
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does anyone how to make a MicrobiomeMarker object form phyloseq in Rstudio?

Im making analysis of microbiome with qiime2 and i want to make a normalization and a lefse analysis with MicrobiomeMarker, but i'm in troubles because when i try to make a microbiomemarker object i got error messages. here the…
kevin SalOrt
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Find samples containing a specific OTU

In my phyloseq tax_table i have some interesting taxa I want to look further into. I want to use OTU number or taxonomic name to figure out which samples have this taxa present. I could just use the OTU# corresponsing to the taxa in tax_table and…
sondre
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Is there a max. number of sample variables (imported as metadata file) that can be included in a phyloseq analysis to create an ordination plot?

I am trying to create an ordination plot with phyloseq data: phyloseq-class experiment-level object otu_table() OTU Table: [ 7934 taxa and 45 samples ] sample_data() Sample Data: [ 45 samples by 37 sample variables ] tax_table() …
djdetweiler
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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…
Sam Reynoso
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Trying to generate ASV table from phyloseq

I recognize most people have the opposite problem. But I'm trying to create an ASV table, with column names as "identified OTUs" (aka the column name is drawn from the taxonomy information from GlobalPatterns@tax.table, rather than just being the…
carrollk2015
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Failing to get individual boxplot intervals for sample locations for phylosq object

I have a phyloseq object containg an otu_table, tax_table and sam_data.physeq is the phyloseq object. I want to use following code: plot_richness(physeq, x ="Location" , measures = c("Observed", "Shannon")) + geom_boxplot() Location is a column in…
sondre
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