[R] Row names and matrixs

From: nielsen4897 <lindseynielsenpc_at_gmail.com>
Date: Wed, 11 May 2011 19:23:33 -0700 (PDT)


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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Received on Thu 12 May 2011 - 03:19:34 GMT

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