我有以下代码:
library(gplots)
library(RColorBrewer);
setwd("~/Desktop")
mydata <- mtcars
hclustfunc <- function(x) hclust(x, method="complete")
distfunc <- function(x) dist(x,method="euclidean")
d <- distfunc(mydata)
fit <- hclustfunc(d)
clusters <- cutree(fit, h=100)
nofclust.height <- length(unique(as.vector(clusters)));
# Colorings
hmcols <- rev(redgreen(2750))
selcol <- colorRampPalette(brewer.pal(12,"Set3"))
selcol2 <- colorRampPalette(brewer.pal(9,"Set1"))
clustcol.height = selcol2(nofclust.height);
heatmap.2(as.matrix(mydata),
trace='none',
dendrogram='both',
key=F,
Colv=T,
scale='row',
hclust=hclustfunc, distfun=distfunc, col=hmcols,
symbreak=T,
margins=c(7,10), keysize=0.1,
lwid=c(5,0.5,3), lhei=c(0.05,0.5),
lmat=rbind(c(5,0,4),c(3,1,2)),
labRow=rownames(mydata),
#ColSideColors=clustcol.height[clusters], # This line doesn't work
RowSideColors=clustcol.height[clusters])
其中产生如下图:
我想要做的是在行和列上执行聚类,并在树形图旁边显示聚类条(RowSideColors和ColSideColors)。我怎样才能做到这一点?
目前我只能成功展示RowSideColors
但 <{1}} ColSideColors
。
答案 0 :(得分:6)
为了显示RowSideColors
和ColSideColors
,您必须分别获取矩阵的行和列的群集分配。目前,对象“群集”包含仅与行对应的群集。
# set the custom distance and clustering functions, per your example
hclustfunc <- function(x) hclust(x, method="complete")
distfunc <- function(x) dist(x, method="euclidean")
# perform clustering on rows and columns
cl.row <- hclustfunc(distfunc(mydata))
cl.col <- hclustfunc(distfunc(t(mydata)))
# extract cluster assignments; i.e. k=8 (rows) k=5 (columns)
gr.row <- cutree(cl.row, 8)
gr.col <- cutree(cl.col, 5)
# require(RColorBrewer)
col1 <- brewer.pal(8, "Set1")
col2 <- brewer.pal(5, "Pastel1")
# require(gplots)
heatmap.2(as.matrix(mydata), hclustfun=hclustfunc, distfun=distfunc,
RowSideColors=col1[gr.row], ColSideColors=col2[gr.col])
您可以使用plot(cl.row)
和plot(cl.col)
检查群集先验。您也可以使用RColorBrewer
库来选择最合适的颜色编码。可能是顺序调色板可能更好,以避免过度着色。