无法找到函数“distance”的继承方法；对于签名“矩阵”、“字符”，但它是 df？

Question

这是我根据 @Till 请求实现该函数的所有代码！

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){

请注意，整个函数逐字来自 Stegen_etal_ISME_2013 github，链接如下和此处 。

我在此处链接的此函数中收到错误

    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 

。

我的参数是一个没有字符串的data.frame（下面的dput()）？据我了解，错误是说函数 distance () 不能用矩阵或字符串计算，我同意......

因此，我不确定为什么 distance () 无法操作使用我的参数，如果我正确地解释了错误。

谢谢。

这是我的 Qiime2 OTU table.qza 链接到此 Dropbox 文件，我的根树链接到此处，以及我的分类链接这里 重新创建我的 phyloseq 对象。

Answer 1

错误消息实际上试图传达的是您的矩阵具有字符值，而您调用的函数无法处理它。 data.frame 中的第一列是字符列。

如果您的数据框名为 ex_otu_ord，请尝试以下操作：

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

然后再次尝试调用 ex_otu_ord 上的函数。