我有一组数据,其中一些元素的值是NA。 我的目标是在不删除包含NA的行的情况下进行聚类。
我知道daisy
中的gower
距离测量可以允许这种情况。
但为什么我的下面的代码不起作用呢?
如果有其他替代方案,我也欢迎。
# 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
最终,我希望能够使用允许NA值的数据来执行层次聚类。
更新
使用as.numeric
将上面的例子转换为数字型数据是可行的。
但是,为什么从文本文件中读取时这段代码会失败呢?
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
~
NA
不同。但除此之外,当NA是其中一个值时,您建议如何定义两点之间的距离? - Dasondaisy
负责这个:http://stat.ethz.ch/R-manual/R-devel/library/cluster/html/daisy.html - neversaint