Hi all -
I am NEW to R and NEW to any type of programming. I am making heatmaps
using the heatmap.2 function within gplots package. At present, when the
heatmap is plotted it uses the row identifiers as 1,2,3,4...etc. However, I
much rather use my own labels. I was told my another well-versed R
programmer to use the follow script:
x<-as.matrix(test1[,-1]) ## skip column 1
rownames(x)<- test[1,]
heatmap(x, scale="none")
This was for data set up in 4 columns such as when you read the data in R it
looks like:
Loci Cont NaCl Peg
1 0231 2.1 4.2 4.1
2 1253 4.1 2.3 2.3
3 8167 5.7 1.1 3.4
Using the script above and this dataset it worked well - the Loci was used
as the row labels rather than the numbers assigned by R.
Looking at the data after this script it looks like:
Loci Cont NaCl Peg
0231 0231 2.1 4.2 4.1
1253 1253 4.1 2.3 2.3
8167 8167 5.7 1.1 3.4
Now, I want to do the same thing BUT my dataset looks like this:
Loci NaCl Peg
1 0231 23.2 34.1
2 1253 25.3 21.3
3 8167 21.1 38.4
When I put in the script
x<-as.matrix(test1[,-1]) ## skip column 1
rownames(x)<- test[1,]
heatmap(x, scale="none")
This is what follows (after looking at the dataset change)
NaCl Peg
[1,] 23.2 34.1
[2,] 25.3 21.3
[3,] 21.1 38.4
If I alter the -1 in the x<-as.matrix(test1[,-1]) line it will 'skip' other
columns but not the first one.
What do I need to enter to make the dataset look like ?
Loci NaCl Peg
0231 0231 23.2 34.1
1253 1253 25.3 21.3
8167 8167 21.1 38.4
Please explain the answer and WHAT the #'s inside the [] mean!
Thanks
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