在R中缩放树状图

时间:2015-05-25 09:13:07

标签: r height cut dendrogram

我想绘制平均连锁聚类产生的树状图。对象之间的成对距离都在0.901.0之间。结果是一棵树,你几乎看不到高度差异。有没有办法放大或缩放,以便存在的差异占用图的整个高度?

literature.csv

file,./doyle_the_adventures_of_sherlock_holmes.txt,./doyle_the_hound_of_the_baskervilles.txt,./fitzgerald_the_beautiful_and_the_damned.txt,./fitzgerald_this_side_of_paradise.txt,./lawrence_sons_and_lovers.txt,./lawrence_the_white_peacock.txt
./doyle_the_adventures_of_sherlock_holmes.txt,0.0007791468073787889,,,,,
./doyle_the_hound_of_the_baskervilles.txt,0.9156855685890994,0.0009740377963077595,,,,
./fitzgerald_the_beautiful_and_the_damned.txt,0.9359979946307857,0.9458024711323867,0.0006671087104182165,,,
./fitzgerald_this_side_of_paradise.txt,0.9248203932273336,0.9283132318706644,0.924584371057994,0.0007603851058105121,,
./lawrence_sons_and_lovers.txt,0.9448158441623475,0.9537187067420674,0.9361454789983296,0.9439788534658211,0.0006760309471944716,
./lawrence_the_white_peacock.txt,0.9340464226303858,0.9441049465183027,0.9315142154801566,0.9353349824600719,0.9286554853294131,0.0006852207789969058

R代码:

library(ape) # for as.phylo function

distances <- "distance_matrices/literature.csv"

distance_matrix <- as.dist( as.matrix( read.csv(distances, row.names=1 ) ) )
clustering <- hclust(distance_matrix, method="average" )

pdf("plots/literature-average.pdf")
plot( as.phylo(clustering) )
dev.off()

结果:

literature clustered with average linkage

0 个答案:

没有答案