[R] Row names and matrixs

[Bert Gunter]

Dear Anonymous/Lindsey Nielsen(?):

While it would not be hard to answer your questions, given your
admitted lack of programming or R experience, approaching your
ignorance piecemeal in this fashion does not seem to be a sensible way
to learn either. Instead, please start by reading the "Introduction to
R" tutorial that comes with the software and working through its
examples carefully. More than likely, this will get you well on your
way and also allow you gain access to many more or R's capabilities.
If you analyze data as part of your career, you won't regret this
investment.  You will also be able to use R's native Help system and
search capabilities, which much of the time will provide you the
information you need to solve your difficulties.

After you have done this, you should also be able to seek the help of
this list more effectively when you are stumped (as most of us are
from time to time), thus wasting both less of both your time and ours.

Cheers,
Bert

On Wed, May 11, 2011 at 7:23 PM, nielsen4897 <lindseynielsenpc at gmail.com> wrote:
> 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
>
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Row-names-and-matrixs-tp3516372p3516372.html
> Sent from the R help mailing list archive at Nabble.com.
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
"Men by nature long to get on to the ultimate truths, and will often
be impatient with elementary studies or fight shy of them. If it were
possible to reach the ultimate truths without the elementary studies
usually prefixed to them, these would not be preparatory studies but
superfluous diversions."

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics