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我陷入了层次聚类的问题。我想使用相关距离方法（d_mydata=dist(1-cor(t(mydata))）和 ward.D2 作为聚类方法来制作树状图和热图。

作为包 pheatmap 中的一个小工具，您可以在左侧绘制树状图以可视化集群。

我的分析流程是这样的：

  1. 创建树状图
  2. 测试有多少簇是最优的（k）
  3. 提取每个集群中的主题
  4. 创建热图

当热图中绘制的树状图与之前绘制的树状图不同时，即使方法相同，我也会感到惊讶。

所以我决定用之前由 cutree 分类的集群创建一个 pheatmap 着色，并测试颜色是否对应于树状图中的集群。

这是我的代码：

# Create test matrix
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")
test<-as.data.frame(test)

# Create a dendrogram with this test matrix
dist_test<-dist(test)
hc=hclust(dist_test, method="ward.D2")

plot(hc)

dend<-as.dendrogram(hc, check=F, nodePar=list(cex = .000007),leaflab="none", cex.main=3, axes=F, adjust=F)


clus2 <- as.factor(cutree(hc, k=2)) # cut tree into 2 clusters
groups<-data.frame(clus2)
groups$id<-rownames(groups)


#-----------DATAFRAME WITH mydata AND THE CLASSIFICATION OF CLUSTERS AS FACTORS---------------------
test$id<-rownames(test)
clusters<-merge(groups, test, by.x="id")
rownames(clusters)<-clusters$id

clusters$clus2<-as.character(clusters$clus2)
clusters$clus2[clusters$clus2== "1"]= "cluster1"
clusters$clus2[clusters$clus2=="2"]<-"cluster2"


plot(dend, 
 main = "test", 
 horiz =  TRUE, leaflab = "none")



d_clusters<-dist(1-cor(t(clusters[,7:10])))
hc_cl=hclust(d_clusters, method="ward.D2")



annotation_col = data.frame( 
  Path = factor(colnames(clusters[3:12]))
)
  rownames(annotation_col) = colnames(clusters[3:12])



annotation_row = data.frame(
    Group = factor(clusters$clus2)
)
rownames(annotation_row) = rownames(clusters)

# Specify colors
ann_colors = list(
  Path= c(Test1="darkseagreen", Test2="lavenderblush2", Test3="lightcyan3", Test4="mediumpurple", Test5="red", Test6="blue", Test7="brown", Test8="pink", Test9="black", Test10="grey"), 
  Group = c(cluster1="yellow", cluster2="blue")
)



require(RColorBrewer)
library(RColorBrewer)
cols <- colorRampPalette(brewer.pal(10, "RdYlBu"))(20)
library(pheatmap)
pheatmap(clusters[ ,3:12], color =  rev(cols), 
     scale = "column",
     kmeans_k = NA,
     show_rownames = F, show_colnames = T,
     main = "Heatmap CK14, CK5/6, GATA3 and FOXA1 n=492 SCALE",
     clustering_method = "ward.D2",
     cluster_rows = TRUE, cluster_cols = TRUE,
     clustering_distance_rows = "correlation", 
     clustering_distance_cols = "correlation",
     annotation_row = annotation_row, 
     annotation_col = annotation_col,  
     annotation_colors=ann_colors
)

热图

有同样问题的人吗？我犯了一个愚蠢的错误吗？

先感谢您

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