Try placing the column names into labCol and the rownames into labRow
e.g.heatmap.2(mat,dendrogram=c("none"),
Rowv=F, Colv=F, labRow = seq(-7.5,7.5,by=5), labCol=seq(-3,3,by=2))
Schalk Heunis
On Thu, Sep 17, 2009 at 3:53 PM, bioinformatics_guy <wwwhite...@gmail.com>wrote:
>
> Schalk,
>
> Thats a great function! The only question is, is it as flexible as
> heatmap.2?
>
> I figured out how to get it from rearranging the rows and columns but I
> can't figure out how to label the rows and columns? What I like about the
> heatmap.2 is that it gives a grid and histogram of the heatmap which is
> nice.
>
> I'm trying to
>
> library(gplots)
> data=read.table("filein.txt",header=FALSE)
> mat=as.matrix(data)
> heatmap.2(mat,dendrogram=c("none"),trace=c("none"),Rowv=F,Colv=F)
>
> which works but labels my columns V1 thru V21 and rows 1-21. Id like them
> to be different an under the man pages for heatmap.2 it states:
>
> # Row/Column Labeling
> margins = c(5, 5),
> ColSideColors,
> RowSideColors,
> cexRow = 0.2 + 1/log10(nr),
> cexCol = 0.2 + 1/log10(nc),
> labRow = NULL,
> labCol = NULL,
>
> So I'm adding cexRow=30-3(nr) (as I want it to decrement by 3 for each row
> but R spits back an error say nr is not recognized. I was looking at other
> help pages but couldn't find out how to lable the axis the way I wanted to.
>
> Schalk Heunis wrote:
> >
> > Hi bioinformatics_guy
> > I think you are looking for the "image" function:
> > image(mat)
> >
> > The heatmap.2 function does hierarchical clustering on rows and columns
> > and
> > then orders the rows and columns according to the results of the
> > clustering.
> > Image simply plots the matrix.
> >
> > HTH
> > Schalk Heunis
> >
> >
> > On Thu, Sep 17, 2009 at 2:23 PM, bioinformatics_guy
> > <wwwhite...@gmail.com>wrote:
> >
> >>
> >> I have a file of the following form
> >>
> >> -11 -10 -9 -8
> >> -10 -9 -8 NA
> >> -9 -7 NA NA
> >> -8 NA NA NA
> >>
> >> So basically a NxN matrix of log scores. I want to get a heatmap of
> >> these
> >> log scores but I'm having a problem.
> >>
> >> I'm using the following code
> >>
> >> library(gplots)
> >> data=read.table("filein.txt",header=FALSE)
> >> mat=as.matrix(data)
> >> heatmap.2(mat,dendrogram=c("none"))
> >>
> >> But on the picture, it rearranges all my row,columns. I want it the y
> >> axis
> >> to be labeled from [10,-10] and the x axis to be the same [-10,10] so
> >> that
> >> the bottom left cell is -10,-10 and the top right cell is 10,10 -- which
> >> is
> >> the way the matrix is laid out. Why is it rearranging my cells?
> >>
> >> --
> >> View this message in context:
> >>
> http://www.nabble.com/heatmap.2%28%29-problems-with-re-ordering-of-rows-and-columns-tp25490249p25490249.html
> >> Sent from the R help mailing list archive at Nabble.com.
> >>
> >> ______________________________________________
> >> R-help@r-project.org 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.
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org 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.
> >
> >
>
> --
> View this message in context:
> http://www.nabble.com/heatmap.2%28%29-problems-with-re-ordering-of-rows-and-columns-tp25490249p25491683.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org 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.
>
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