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I am trying to create a heatmap with an external dendrogram using the ComplexHeatmap library .

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().

enter image description here Plot created form the plot command

lovalery
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Mike Eugeniou
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1 Answers1

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The problem is that after all the transformations:

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. The quick fix would be to add the following line to restore initial order:

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.

ouflak
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Stefano Barbi
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  • I think you must be rigth. Because if i change the order of the commands and create the dendrogram object after i create the 0-1 dataframe ,instead the opposite, while changing the first argument of stringdist::stringdistmatrix(df$rel...) with stringdist::stringdistmatrix(rownames(df)) it works fine. – Mike Eugeniou Feb 04 '22 at 16:12