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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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Calculate distances between groups (group-comparison using UniFrac or Bray-Curtis)

I'd like to ask how to calculate distances between groups using weighted UniFrac or Bray-Curtis method in R. I already got distances between each sample using UniFrac…
So young Yeo
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Error in betadisper(dissimilarity_matrix ~ Group) : distances 'd' must be a 'dist' object

I get the error as in the title, when I try to do betadisper on my dissimilarity matrix. When looking at my environment it clearly says 'dist'. as.dist() doesn't help #fhf is a phyloseq object veganotu = function(physeq) { require("vegan") …
Arne Claeys
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Pass arguments to the R Phyloseq subset_taxa wrapper

I'll explain the end goal, and what I'm trying as a test first. (Because I'm likely going about it the wrong way.) I am using the phyloseq package to visualize microbiome data. I want to "automate" it to an extent by having users choose levels of…
Steve
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Using an r variable in a parameter that expects a function

I have a loop through column names which returns a variable character. I would like to use the variable in a parameter that expects a function. Not Working i = "Cooling" temp = phyloseq_to_deseq2(p2, ~i)} Works temp = phyloseq_to_deseq2(p2,…
Cody Glickman
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Order x axis by one then another parameter and plot in ggplot (phyloseq)

I am trying to graph my phyloseq/deseq2 data output (Log2FoldChange on y and Species name on x) in ggplot and I would like to be able to order them by autotrophs and heterotrophs as well as max-min value. I have a column I added into the Taxa file…
Megan Ladds
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Is there a way to break up (modularize) code in an RShiny app?

I am building an application on RShiny using the Phyloseq library, and the code is starting to become unmanageable. I saw other code examples where programmers like Joey711 source their code from other files. Here is an example: # Bar …
Ariel A
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How can I re-order my X-axis so that my Samples are grouped based on the Group they belong to

Basically I have some graphs I am working on and they are facetted by Groups (there are four). The X axis are samples but as you can see my Groups are still showing blank samples from other groups. Is there a way to change this? I have posted my…
user3105519
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Attempting to add confidence ellipses to NMDS gives error "Error in cov.wt(X, W) : 'x' must contain finite values only"

I am attempting to add 95% confidence ellipse to an NMDS plot using the vegan package and function "ordiellipse" and keep getting the same error message. The ordination looks like this: microcosm_nmds <- ordinate(physeq = physeq_bac1, method =…
Kt McBride
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How to use new grouped together values in a plot

I have combine different values which means the same, under the variable "Wine_type" Mock Neg Neg1PCR NegPBS red Red RedWine water Water white White 1 9 1 1 2 18 4 3 4 2 …
Rasmus
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How to combine multiple variable data to a single variable data?

After making my data frame, and selecting the variables i want to look at, i face a dilemma. The excel sheet which acts as my data source was used by different people recording the same type of data. Mock Neg Neg1PCR Neg2PCR NegPBS red …
Rasmus
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Merging OTU table and phylogenetic tree with phyloseq

I'm trying to create a phyloseq class object with an OTU table, taxa names, sample data and a phylogenetic tree using the following commands ps <- phyloseq(otu_table(seqtab.nochim, taxa_are_rows=F), tax_table(taxa), …
aboyd
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Make variable a name

I created my first function and I'm super proud of myself, but I'm trying to make it better. It goes through an abundance table, identifies the most abundant column in each row, and then gives me a name for that column that correlates with another…
Samaj Oruel
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Max Column for each Row

I'm an R novice, so I can't make a sample data frame for you, for which I apologize. However, I'm doing bacterial community analysis and I have a table that has species for each column and each sample for each row. Each column is an identifier for…
Samaj Oruel
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Coloring Rarefaction curve lines by metadata (vegan package) (phyloseq package)

First time question asker here. I wasn't able to find an answer to this question in other posts (love stackexchange, btw). Anyway... I'm creating a rarefaction curve via the vegan package and I'm getting a very messy plot that has a very thick black…
Samaj Oruel
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phyloseq complaining about functions missing from vegan

I'm working through this tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html In Ubuntu 16.04, I'm getting errors any time I try to use one of the ordination functions. Update: It does work for me in Windows 10, R…
Mark Miller
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