CODEWITHSUNDEEP
rannotationspheatmap
Kwnwps
Kwnwps

Reputation: 363

Cluster annotations using pheatmap

So, I am trying to create a pretty heatmap with pheatmap function in R.

I want to have coloured bars where the dendrogram stops and the graph starts in order to annotate the different clusters. Like a horizontal thick line running through columns and changes colours when it pass to another cluster. It's pretty common I think. But I can't figure out the 'annotations' in pheatmap. Any ideas?

    structure<-matrix(rnorm(10000),ncol=100,nrow=100)
    dist_structue<-dist(structure)
    clustering<-hclust(dist)   
    cols2 = colorRampPalette(c('green','white','red'))(20) 
    annotation <- data.frame(Var1 = factor(cutree(clustering, k = 4))    
    heat_chem <- pheatmap(as.matrix(dist_structure),
                 clustering_distance_rows=dist_structure, 
                 cellwidth = 4, cellheight = 4, cluster_rows=T,cluster_cols=T, legend = T,
                 clustering_distance_cols = dist_structure, show_rownames = TRUE,
                 fontsize_row = 5, annotation_row = annotation,
                 show_colnames = FALSE, cutree_cols = 4, cutree_rows=4, 
                 color = cols2,
                 main = 'Heatmap')

Upvotes: 0

Views: 2044

Answers (1)

pcantalupo
pcantalupo

Reputation: 2226

The rownames of annotation are not matching the rownames of as.matrix(dist_structure)

Upvotes: 2

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