我有一个在其元素中包含一些NA值的数据。我想做的是在不删除存在NA的行的情况下执行聚类。
我了解允许这种情况的gower
距离测量daisy
。但是,为什么下面的代码不起作用?我欢迎使用“雏菊”以外的其他替代方法。
# 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);
我收到的错误消息是这样的:
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
归根结底,我想对NA允许的数据执行分层聚类。
更新资料
使用as.numeric
上面的示例进行转换。但是,为什么从文本文件读取时此代码失败?
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
〜
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)引起的。您可以将它们转换为数字:
mydata <- apply( mtcars, 2, as.numeric )
d <- distfunc(mydata)
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