Hi
I am doing a cluster analysis and I have some troubles with the label names.
In the text file I have my data in, the first row contains the names of the
samples. They are called "FFPE Tumor 2", "Fresh Frozen Tumor 2" etc.
But when the cluster is made the label names contains periods instead of space
in the name.
I can't figure out how to change this, so I get spaces in the label names.
I hope someone can help?
The code I have used is:
#Set where you want to save your images/clusters
setwd("/Users/gban/Desktop/Lung Cancer/PAXgene article figures/PAXgene cluster
+ Venn analysis")
#Read in data
data<-read.table("/Users/gban/Desktop/Lung Cancer/PAXgene article
figures/PAXgene cluster + Venn
analysis/BetaValue_ALL_tumo1_dup2_Codename.txt",sep="\t",dec=",",header=TRUE)
# Throw out rows with missing values.
data = na.omit(data)
#Turn the data into a matrix
Data_matrix<-as.matrix(data)
#Calculate the distance
Data_dist<-dist(t(data))
#Make the cluster
hc = hclust(Data_dist,method="ward")
# reduced label size
par(cex=0.7, mar=c(5, 8, 4, 1))
plot(hc, xlab="", ylab="", main="", sub="", axes=FALSE)
par(cex=1)
title(xlab="", ylab="", main="Cluster analysis")
axis(2)
The cluster output:
[cid:D57BB82B-3ACF-4681-BCA8-D8202EA34294@eduroam.net.au.dk]
Kind regards
Gitte Brinch Andersen
Ph.d student
Department of Biomedicine
Wilhelm Meyers Allé 4
Aarhus Universitet
DK-8000 Aarhus C
E-mail: gitt...@hum-gen.au.dk<mailto:gitt...@hum-gen.au.dk>
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