[英]External dendrogram does not keep the same formation when using it for cluster_rows in complexheatmap
I am trying to create a heatmap with an external dendrogram using the ComplexHeatmap
library.我正在尝试使用ComplexHeatmap
库创建带有外部树状图的热图。
df <- data.frame(genes=c("G1","G2","G3","G4","G5","G6","G7","G8","G9","G10",
"G11","G1","G12","G4","G15","G6","G17","G8","G1","G2"),
rel=c("A111SD","G422ER","A112SA","B457EE","B33","N124A","F124A",
"G900GG","I332LP","I332LO",
"M332LP","A322TR","C14SA","B467ET","Z653","R124T","F334A",
"G901GZ","R330TP","L982LP"))
df_dist <- stringdist::stringdistmatrix(df$rel,useNames = T)
df_hclust <- hclust(df_dist)
plot(df_hclust)
df$Id <- seq.int(nrow(df))
df <- spread(df,genes,Id)
rownames(df) <- df$rel
df$rel<- NULL
df[!is.na(df)] <- 1
df[is.na(df)] <- 0
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")
library(ComplexHeatmap)
Heatmap(as.matrix(df),cluster_rows = df_hclust,cluster_columns = F)
The created heatmap has a different dendrogram from the one built using plot()
.创建的热图与使用plot()
构建的热图具有不同的树状图。
the problem is that after all the transformations问题是,经过所有的转变
df$Id <- seq.int(nrow(df))
df <- spread(df,genes,Id)
rownames(df) <- df$rel
df$rel<- NULL
df[!is.na(df)] <- 1
df[is.na(df)] <- 0
the data.frame df has no longer the initial order. data.frame df 不再具有初始顺序。 The quick fix would be to add the following line to restore initial order:快速解决方法是添加以下行以恢复初始顺序:
df <- df[rownames(as.matrix(df_dist)),]
However, I suggest you to avoid reassigning to the same variable because it easily leads into these kinds of problems.但是,我建议您避免重新分配给同一个变量,因为它很容易导致这类问题。
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