Question

I am programming a heatmap in R based on a csv file. This contains the following information:

NAME,metformin,metformin,phenformin,phenyl biguanide,metformin,estradiol
Adenocarcinoma of lung,0,0,0,-1.834006462,1.715939688,0
Adenocarcinoma of lung,1.995916353,0,0,0,0,0
Thymic carcinoma,1.154056722,1.106488961,0,1.145126548,0,-1.14095315
alpha-1-Antitrypsin deficiency,0,0,0,0,-1.917025669,-1.974151858

So I want to create a heatmap in which in the name of the rows appears the labels: Adenocarcinoma of the lung, Adenocarcinoma… etc. I am doing this steps:

hm<-read.csv("heatmap1.csv",sep=",")
row.names(hm)<-hm$NAME
hm<-hm[,2:7]
hm_matrix<-data.matrix(hm)
heatM<-heatmap(hm_matrix, Rowv=NA, Colv=NA, col = cm.colors(256), scale="column", margins=c(5,10))

The problem I got is in the line that says:

row.names(hm)<-hm$NAME

Error in `row.names<-.data.frame`(`*tmp*`, value = c(1L, 1L, 3L, 2L)) : 
  duplicate 'row.names' are not allowed

I know that I have a duplicated name, but I really need that data appears in the heatmap because the measure levels (the quantities) are different even if they are from the same disease.

Thanks for the help

Answer 1

You can use make.unique to make unique versions of the names

row.names(hm) <-  make.unique(as.character(hm$NAME))