CODEWITHSUNDEEP
rplotheatmap
pdubois
pdubois

Reputation: 7800

How to reduce the gap between dendrogram and heatmap in R

The following figure enter image description here

Is generated with this code

library(gplots)
setwd("~/Desktop/");
data <- read.table(file='http://pastebin.com/raw.php?i=ZaGkPTGm', 
                   header=TRUE, row.names=1)

mat <- as.matrix(data[,-1])
z <- t(scale(t(mat))) 


# set custom distance and clustering functions
hclustfunc <- function(x) hclust(x, method="complete")
distfunc <- function(x) dist(x,method="maximum")

# obtain the clusters
fit <- hclustfunc(distfunc(z))
clusters <- cutree(fit, 5) 

# require(gplots)
pdf(file='heatmap.pdf', height=50, width=90)
heatmap.2(z, trace='none', dendrogram='row', Colv=F, scale='row', 
             hclust=hclustfunc, distfun=distfunc, col=greenred(256), symbreak=T,
             margins=c(10,20), keysize=0.5, labRow=data$Gene.symbol,
             lwid=c(1,0.05,1), lhei=c(0.03,1), lmat=rbind(c(5,0,4),c(3,1,2)),
             RowSideColors=as.character(clusters))
dev.off()

What I'm to do is to reduce the gap between the dendrogram and the rowside color of the heatmap. How can I achieve that?

The only requirement is that the dimension of the dendrogram and paper size must be kept as it is.

Upvotes: 3

Views: 1026

Answers (1)

plannapus
plannapus

Reputation: 18759

One solution is to adjust globally the x-axis so that it fits the data range:

par(xaxs="i")
heatmap.2(z, trace='none', dendrogram='row', Colv=F, scale='row', 
         hclust=hclustfunc, distfun=distfunc, col=greenred(256), symbreak=T,
         margins=c(10,20), keysize=0.5, labRow=data$Gene.symbol,
         lwid=c(1,0.05,1), lhei=c(0.03,1), lmat=rbind(c(5,0,4),c(3,1,2)),
         RowSideColors=as.character(clusters))

Upvotes: 1

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