如何在不删除R中存在NA的行的情况下执行聚类

Question

我有一个数据,其元素中包含一些NA值.我想要做的是执行群集而不删除 存在NA的行.

我理解gower距离测量daisy允许这样的情况.但为什么我的代码不起作用？我欢迎除"雏菊"之外的其他选择.

# plot heat map with dendogram together.

library("gplots")
library("cluster")


# Arbitrarily assigning NA to some elements
mtcars[2,2] <- "NA"
mtcars[6,7]  <- "NA"

 mydata <- mtcars

hclustfunc <- function(x) hclust(x, method="complete")

# Initially I wanted to use this but it didn't take NA
#distfunc <- function(x) dist(x,method="euclidean")

# Try using daisy GOWER function 
# which suppose to work with NA value
distfunc <- function(x) daisy(x,metric="gower")

d <- distfunc(mydata)
fit <- hclustfunc(d)

# Perform clustering heatmap
heatmap.2(as.matrix(mydata),dendrogram="row",trace="none", margin=c(8,9), hclust=hclustfunc,distfun=distfunc);

我得到的错误信息是这样的:

    Error in which(is.na) : argument to 'which' is not logical
Calls: distfunc.g -> daisy
In addition: Warning messages:
1: In data.matrix(x) : NAs introduced by coercion
2: In data.matrix(x) : NAs introduced by coercion
3: In daisy(x, metric = "gower") :
  binary variable(s) 8, 9 treated as interval scaled
Execution halted

在一天结束时,我想用NA允许的数据执行分层聚类.

更新

使用as.numeric上面的示例进行转换.但是,从文本文件中读取时,为什么此代码失败？

library("gplots")
library("cluster")

# This time read from file
mtcars <- read.table("http://dpaste.com/1496666/plain/",na.strings="NA",sep="\t")

# Following suggestion convert to numeric
mydata <- apply( mtcars, 2, as.numeric )

hclustfunc <- function(x) hclust(x, method="complete")
#distfunc <- function(x) dist(x,method="euclidean")
# Try using daisy GOWER function 
distfunc <- function(x) daisy(x,metric="gower")

d <- distfunc(mydata)
fit <- hclustfunc(d)

heatmap.2(as.matrix(mydata),dendrogram="row",trace="none", margin=c(8,9), hclust=hclustfunc,distfun=distfunc);

我得到的错误是这样的:

  Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
Error in hclust(x, method = "complete") : 
  NA/NaN/Inf in foreign function call (arg 11)
Calls: hclustfunc -> hclust
Execution halted

〜

Answer 1

该错误是由于数据中存在非数字变量(编码为字符串的数字).您可以将它们转换为数字:

mydata <- apply( mtcars, 2, as.numeric )
d <- distfunc(mydata)