CODEWITHSUNDEEP
rdataframematrixcharacter
Geomicro
Geomicro

Reputation: 454

unable to find an inherited method for function 'distance' for signature '"matrix", "character"', but it's a df?

Here is all my code leading up to the function as per @Till request!

library("phyloseq")
library("qiime2R")
library("vegan")

# read in phyloseq objects from qiime
physeq<-qza_to_phyloseq(
  features="~/Documents/qiime2-analyses/CRD/fresh_run/table.qza",
  tree="~/Documents/qiime2-analyses/CRD/fresh_run/rooted-tree.qza",
  "~/Documents/qiime2-analyses/CRD/fresh_run/taxonomy.qza",
  metadata = "crd-metadata.txt")

# Clean out unwanted taxa annotations. Base script removes endozoicimonaceae, escherischia,
# and shigella contaminates
physeq <- subset_taxa(physeq, Family!="f__Endozoicimonaceae")
physeq <- subset_taxa(physeq, Family!="f__Enterobacteriaceae")
physeq <- subset_taxa(physeq, Family!="f__mitochondria")
physeq <- subset_taxa(physeq, Class!="c__Chloroplast")

#pull out otu table
otu_table <- (as.data.frame(otu_table(physeq)))

# rotate otu matrix layout
rownames(otu_table) <- factor(rownames(otu_table), levels = rownames(otu_table))
otu_ord <- as.data.frame(t(otu_table[rowSums(otu_table)!=0, ]))

# remove any rows or columns with only 0s
otu_ord <- otu_ord[, colSums(otu_ord !=0)>0]
otu_ord <- otu_ord[rowSums(otu_ord[])>0,]

#edits from observations of this StO chat
rownames(otu_ord) <- gsub("sample-", "", rownames(otu_ord))
rownames(otu_ord) <- as.numeric(rownames(otu_ord))
otu_ord <- as.matrix(otu_ord)

#the args of the function
raup_crick_abundance = function(spXsite=otu_ord, plot_names_in_col1=TRUE, 
                                classic_metric=FALSE, split_ties=TRUE, 
                                reps=9999, set_all_species_equal=FALSE, 
                                as.distance.matrix=TRUE, report_similarity=FALSE){

Please note the whole function is verbatim from Stegen_etal_ISME_2013 github linked below and here.

I am receiving the error

    Error in (function (classes, fdef, mtable)  : 
      unable to find an inherited method for function ‘distance’ for signature ‘"matrix", "character"’
Called from: (function (classes, fdef, mtable) 
{
    methods <- .findInheritedMethods(classes, fdef, mtable)
    if (length(methods) == 1L) 
        return(methods[[1L]])
    else if (length(methods) == 0L) {
        cnames <- paste0("\"", vapply(classes, as.character, 
            ""), "\"", collapse = ", ")
        stop(gettextf("unable to find an inherited method for function %s for signature %s", 
            sQuote(fdef@generic), sQuote(cnames)), domain = NA)
    }
    else stop("Internal error in finding inherited methods; didn't return a unique method", 
        domain = NA)
})(list("matrix", "character"), new("nonstandardGenericFunction", 
    .Data = function (physeq, method, type = "samples", ...) 
    {
        standardGeneric("distance")
    }, generic = "distance", package = "phyloseq", group = list(), 
    valueClass = character(0), signature = c("physeq", "method", 
    "type"), default = NULL, skeleton = (function (physeq, method, 
        type = "samples", ...) 
    stop("invalid call in method dispatch to 'distance' (no default method)", 
        domain = NA))(physeq, method, type, ...)), <environment>)
Browse[1]> traceback()
No traceback available

within this function linked here.

My argument is a data.frame (dput() below) with no character strings? As I understand it, the error is saying the function distance () can't be calculated with matrix or character strings, which I agree with...

Therefore, I am unsure why distance () cannot operate with my arg, if I am interpreting the error correctly.

Thank you.

Here is my Qiime2 OTU table.qza linked to this Dropbox file, my rooted tree linked here, and my taxonomy linked here to recreate my phyloseq object.

Upvotes: 0

Views: 1554

Answers (1)

Till
Till

Reputation: 6663

What the error message is actually trying to get across is that your matrix has character values and the function you called can not handle it. The first column in data.frame is a character column.

If your data frame is called ex_otu_ord, try this:

ex_otu_ord <- ex_otu_ord[-1]
ex_otu_ord <- as.matrix(ex_otu_ord)

Then try again to call the function on ex_otu_ord.

Upvotes: 1

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