Sorry, I just realized I didn't send this to the list! (See below)
Thanks for all the help! All is working fine now.
If anyone knows of a more straightforward way to change the "Value" string
for the Key, please let me know (just to satisfy my curiosity). I got it to
work by modifying the source code (specifically, "heatmap.2.R " in the
gplots package).
However, before, I didn't make the call
source("heatmap.2.R")
before I called
source("mysillyheatmap.R")
Making the additional call to " heatmap.2.R" fixed everything.
Thanks again for all your help!
On 7/19/07, Suzanne Matthews <[EMAIL PROTECTED]> wrote:
>
> Thank you all for your prompt replies! The check.names=FALSE parameter
> fixed things entirely.
>
> One more question:
>
> Is there a straightforward way to modify the the "Values" string that
> labels the key to a user-defined value? For example, let's say I want to
> change "Values" to "Silly Values". So far, what I have found that I need to
> do is actually go and change a static string in the source code. Is there a
> more direct way?
>
> Also, after I make the source code change (in gplots package, file:
> heatmap.2.R), how do I have R build from that? If I remember correctly, if
> I put the new heatmap.2.R in my directory, R is supposed to check for
> functions and such there before it goes and builds it from the main source
> code base (located at /usr/bin/R). I am a touch confused on which directory
> is "my" directory, where R will check first. I tried putting the modified
> heatmap.2.R file in the directory that my script is, and where I initially
> run R. But that didn't work!
>
> Is there anything that I should add to my R script that will force it to
> read from that from my directory? If not, which directory should I place
> this in?
>
> My OS is OS X, so I think Unix-based instructions will work.
>
> Thank you once again for your time and patience!
>
> Sincerely,
> Suzanne
>
> On 7/18/07, Moshe Olshansky <[EMAIL PROTECTED]> wrote:
> >
> > I was right saying that my solution was not the best
> > possible!
> >
> > --- Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> >
> > > read.table('temp.txt', check.names = FALSE)
> > >
> > > would be easier (and more general, since make.names
> > > can do more than
> > > prepend an 'X').
> > >
> > > On Wed, 18 Jul 2007, Moshe Olshansky wrote:
> > >
> > > > Hi Suzanne,
> > > >
> > > > My solution (which I am sure is not the best)
> > > would
> > > > be:
> > > >
> > > >> heat <- read.table('temp.txt')
> > > >> heat
> > > > X1905 X1910 X1950 X1992 X2011 X2020
> > > > Gnat 0.08 0.29 0.29 0.37 0.39 0.43
> > > > Snake 0.16 0.34 0.32 0.40 0.41 0.53
> > > > Bat 0.40 0.54 0.52 0.60 0.60 0.63
> > > > Cat 0.16 0.27 0.29 0.39 0.37 0.41
> > > > Dog 0.43 0.54 0.52 0.61 0.60 0.62
> > > > Lynx 0.50 0.57 0.54 0.59 0.50 0.59
> > > >> a<-names(heat)
> > > >> b<-strsplit(a,split="X")
> > > >> w<-unlist(b)
> > > >> w
> > > > [1] "" "1905" "" "1910" "" "1950" ""
> > > > "1992" "" "2011" "" "2020"
> > > >> z <- w[seq(2,length(w),by=2)]
> > > >> z
> > > > [1] "1905" "1910" "1950" "1992" "2011" "2020"
> > > >> names(heat) <- z
> > > >> heat
> > > > 1905 1910 1950 1992 2011 2020
> > > > Gnat 0.08 0.29 0.29 0.37 0.39 0.43
> > > > Snake 0.16 0.34 0.32 0.40 0.41 0.53
> > > > Bat 0.40 0.54 0.52 0.60 0.60 0.63
> > > > Cat 0.16 0.27 0.29 0.39 0.37 0.41
> > > > Dog 0.43 0.54 0.52 0.61 0.60 0.62
> > > > Lynx 0.50 0.57 0.54 0.59 0.50 0.59
> > > >>
> > > >
> > > > Regards,
> > > >
> > > > Moshe.
> > > >
> > > > --- Suzanne Matthews
> > > <[EMAIL PROTECTED]>
> > > > wrote:
> > > >
> > > >> Hello All,
> > > >>
> > > >> I have a simple question based on how things are
> > > >> labeled on my heat map;
> > > >> particularly, there is this annoying "X" that
> > > >> appears before the numeric
> > > >> value of all the labels of my columns.
> > > >>
> > > >> Let's say I have the following silly data, stored
> > > in
> > > >> "temp.txt"
> > > >> 1905 1910 1950 1992 2011
> > > 2020
> > > >> Gnat 0.08 0.29 0.29 0.37 0.39
> > > 0.43
> > > >> Snake 0.16 0.34 0.32 0.40 0.41
> > > 0.53
> > > >> Bat 0.40 0.54 0.52 0.60 0.60
> > > 0.63
> > > >> Cat 0.16 0.27 0.29 0.39 0.37
> > > 0.41
> > > >> Dog 0.43 0.54 0.52 0.61 0.60
> > > 0.62
> > > >> Lynx 0.50 0.57 0.54 0.59 0.5
> > > 0.59
> > > >>
> > > >> I use the following commands to generate my
> > > heatmap:
> > > >> heat <- read.table('temp.txt')
> > > >> x <- as.matrix(heat)
> > > >>
> > > >> heatmap.2(x, keysize=1.2, dendrogram="none",
> > > >> trace="none", Colv = FALSE,
> > > >> main = "Silly Data", labCol=
> > > >> NULL, margin=c(7,8))
> > > >>
> > > >> This generates a very nice heatmap, but there is
> > > one
> > > >> thing I have an issue
> > > >> with: How do I get rid of the 'X' that seems to
> > > come
> > > >> automatically before my
> > > >> numeric column values? I just want those columns
> > > to
> > > >> be labeled 1905, 1910,
> > > >> 1950, and so on. I cannot find anything in the
> > > >> heatmap.2 documentation that
> > > >> suggests how I should do this.
> > > >>
> > > >> Thank you very much for your time, and patience
> > > in
> > > >> reading this!
> > > >>
> > > >> Sincerely,
> > > >> Suzanne
> > > >>
> > > >> [[alternative HTML version deleted]]
> > > >>
> > > >> ______________________________________________
> > > >> R-help@stat.math.ethz.ch mailing list
> > > >> https://stat.ethz.ch/mailman/listinfo/r-help
> > > >> PLEASE do read the posting guide
> > > >> http://www.R-project.org/posting-guide.html
> > > >> and provide commented, minimal, self-contained,
> > > >> reproducible code.
> > > >>
> > > >
> > > > ______________________________________________
> > > > R-help@stat.math.ethz.ch mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > > and provide commented, minimal, self-contained,
> > > reproducible code.
> > > >
> > >
> > > --
> > > Brian D. Ripley,
> > > [EMAIL PROTECTED]
> > > Professor of Applied Statistics,
> > > http://www.stats.ox.ac.uk/~ripley/<http://www.stats.ox.ac.uk/%7Eripley/>
> > > University of Oxford, Tel: +44 1865
> > > 272861 (self)
> > > 1 South Parks Road, +44 1865
> > > 272866 (PA)
> > > Oxford OX1 3TG, UK Fax: +44 1865
> > > 272595
> > >
> >
> >
>
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