Hello Sir I am Saraswati and I am working on whole shotgun metagenomics datasets, for that purpose I profiled the taxonomy using the MetaPhlAn3 software but now I want to use phyloseq package to generate more figures. I saw your code on GitHub to import the metaphlan3 files to phyloseq but I am facing few problems. I am pasting my code here. My main problem is that I need details of importing process as I do not have very good hands-on R programming.

Code should be placed in three backticks as shown below

> library("phyloseq")
> library(readxl)
> library("ggplot2")
> library(curatedMetagenomicData)
> theme_set(theme_bw())
> otumat=read.csv("~/Documents/FLOOR-METAGENOME-NOVASEQ/METAPHLAN-RES/MetaPhlAn3-Final_Res/A1_R12_profile_(copy).txt", sep="\t", strip.white = T, stringsAsFactors = F, row.names=1)
> metaphlanToPhyloseq <- function(
+   metaphlandir=("~/Documents/FLOOR-METAGENOME-NOVASEQ/METAPHLAN-RES/MetaPhlAn3-Final_Res/A1_R12_profile_(copy).txt"),
+   metadat=NULL,
+   simplify=TRUE){
+   ## tax is a matrix or data.frame with the table of taxonomic abundances, rows are taxa, columns are samples
+   ## metadat is an optional data.frame of specimen metadata, rows are samples, columns are variables
+   ## if simplify=TRUE, use only the most detailed level of taxa names in the final object
+   ## metaphlanToPhyloseq("~/Downloads/metaphlan_bugs_list")
+   .getMetaphlanTree <- function(removeGCF=TRUE, simplify=TRUE){
+     if (!requireNamespace("ape")) {
+       stop("Please install the ape package to read Newick trees")
+     }
+     nwkfile <- bzfile(system.file("~/Documents/FLOOR-METAGENOME-NOVASEQ/SUMMARY/mpa_v30_CHOCOPhlAn_201901_species_tree.nwk",
+                                   package="curatedMetagenomicData"))
+    tree <- ape::read.tree(nwkfile)
+     close(nwkfile)
+     if(removeGCF)
+       tree$tip.label <- sub("\|GCF_[0-9]+$", "", tree$tip.label)
Error: '\|' is an unrecognized escape in character string starting ""\|"
>     if(simplify)
+       tree$tip.label <- gsub(".+\|", "", tree$tip.label)
Error: '\|' is an unrecognized escape in character string starting "".+\|"
>     return(tree)
Error: object 'tree' not found
>   }
Error: unexpected '}' in "  }"
>   .joinListOfMatrices <- function(obj) {
+     rnames <- Reduce(union, lapply(obj, rownames))
+     cnames <- names(obj)
+     if (!all(isUnique(cnames))) {
+       stop("Column names are not unique.")
+     }
+     output <- matrix(0,
+                      nrow = length(rnames),
+                      ncol = length(cnames),
+                      dimnames = list(rnames, cnames)
+     )
+     for (i in seq_along(obj)) {
+       output[match(rownames(obj[[i]]), rownames(output)), i] <- obj[[i]][, 1]
+     }
+     return(output)
+   }
>   fnames <- list.files(metaphlandir)
Error in list.files(metaphlandir) : object 'metaphlandir' not found
>   bug.l <- lapply(fnames, function(x){
+     res <- read.delim(file.path(metaphlandir, x), stringsAsFactors = FALSE, row.names = 1)
+     colnames(res) <- x
+     return(res)
+   })
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'X' in selecting a method for function 'lapply': object 'fnames' not found
>   names(bug.l) <- fnames
Error: object 'fnames' not found
>   tax <- .joinListOfMatrices(bug.l)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'Reduce': error in evaluating the argument 'X' in selecting a method for function 'lapply': object 'bug.l' not found
Called from: h(simpleError(msg, call))
Browse[1]>   xnames = rownames(tax)
Error during wrapup: object 'tax' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   shortnames = gsub(".+\|", "", xnames)
Error during wrapup: '\|' is an unrecognized escape in character string starting "".+\|"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   if(simplify){
+     rownames(tax) = shortnames
+   }
Error during wrapup: object 'simplify' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   x2 = strsplit(xnames, split="|", fixed=TRUE)
Error during wrapup: object 'xnames' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   taxmat = matrix(NA, ncol=max(sapply(x2, length)), nrow=length(x2))
Error during wrapup: object 'x2' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   colnames(taxmat) = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species", "Strain")[1:ncol(taxmat)]
Error during wrapup: object 'taxmat' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   rownames(taxmat) = rownames(tax)
Error during wrapup: object 'tax' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   for (i in 1:nrow(taxmat)){
+     taxmat[i, 1:length(x2[[i]])] <- x2[[i]]
+   }
Error during wrapup: object 'taxmat' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   taxmat = gsub("[a-z]__", "", taxmat)
Error during wrapup: object 'taxmat' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   taxmat = phyloseq::tax_table(taxmat)
Error during wrapup: error in evaluating the argument 'object' in selecting a method for function 'tax_table': object 'taxmat' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   otutab = phyloseq::otu_table(tax, taxa_are_rows=TRUE)
Error during wrapup: error in evaluating the argument 'object' in selecting a method for function 'otu_table': object 'tax' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   tree <- .getMetaphlanTree(simplify=simplify)
Error during wrapup: could not find function ".getMetaphlanTree"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   if(is.null(metadat)){
+     metadat <- data.frame(file=fnames, row.names=fnames, stringsAsFactors = FALSE)
+   }
Error during wrapup: object 'metadat' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   res = phyloseq::phyloseq(taxmat, otutab, phyloseq::sample_data(metadat), tree)
Error during wrapup: object 'taxmat' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]>   return(res)
Error during wrapup: object 'res' not found
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Browse[1]> }
Error during wrapup: unexpected '}' in "}"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart


sessionInfo( )