Question

我正在使用R.生成热图我使用了hclust函数并得到了错误： Colv dendrogram doesn't match size of x。

下面是我的代码，它与方形矩阵完美配合。现在我的输入矩阵是400x2000。有人能告诉我为什么会收到这个错误吗？

data <- read.table("mydata.txt",sep="\t",header=TRUE,row.names=1)
data_matrix <- data.matrix(data)
library(gplots)
library("RColorBrewer")
colors <- colorRampPalette(rev(brewer.pal(9, "Blues")) )(255)
hc_dist= dist(data_matrix)
hc_clust= hclust(hc_dist)
hr_dist= dist(t(data_matrix))
hr_clust= hclust(hr_dist)
heatmap.2(data_matrix, col=brewer.pal(11,"RdBu"), labRow=NA, density.info="none", scale="row",trace="none",Colv=as.dendrogram(hc_clust),     Rowv=as.dendrogram(hr_clust))

 Error in heatmap.2(data_matrix, col = brewer.pal(11, "RdBu"), labRow = NA,:Colv dendrogram doesn't match size of x

Answer 1

发表我的评论：

想象一下这个矩阵：

matex<-matrix(1:50,ncol=5)
colnames(matex)<-paste0("col",1:5)
rownames(matex)<-paste0("row",1:10)
head(matex)
#      col1 col2 col3 col4 col5
#row1     1   11   21   31   41
#row2     2   12   22   32   42
#row3     3   13   23   33   43
#row4     4   14   24   34   44
#row5     5   15   25   35   45
#row6     6   16   26   36   46

现在，像你一样计算距离：

hc_dist= dist(matex) # what you think are between columns distances
hr_dist= dist(t(matex)) # what you think are between rows distances

并检查对象hc_dist和hr_dist：

hc_dist
           # row1      row2      row3      row4      row5      row6      row7      row8      row9
# row2   2.236068                                                                                
# row3   4.472136  2.236068                                                                      
# row4   6.708204  4.472136  2.236068                                                            
# row5   8.944272  6.708204  4.472136  2.236068                                                  
# row6  11.180340  8.944272  6.708204  4.472136  2.236068                                        
# row7  13.416408 11.180340  8.944272  6.708204  4.472136  2.236068                              
# row8  15.652476 13.416408 11.180340  8.944272  6.708204  4.472136  2.236068                    
# row9  17.888544 15.652476 13.416408 11.180340  8.944272  6.708204  4.472136  2.236068          
# row10 20.124612 17.888544 15.652476 13.416408 11.180340  8.944272  6.708204  4.472136  2.236068

hr_dist
          # col1      col2      col3      col4
# col2  31.62278                              
# col3  63.24555  31.62278                    
# col4  94.86833  63.24555  31.62278          
# col5 126.49111  94.86833  63.24555  31.62278

实际上，hc_dist包含列距离之间的行距离和hr_dist之间的距离，因此错误（因为行数和列数相同，所以你不会得到方形矩阵）

heatmap.2-错误：Colv树形图与x的大小不匹配

1 个答案: