[R] Analyzing dendograms??

Simon Fear Simon.Fear at synequanon.com
Mon Jan 5 15:44:58 CET 2004


I don't think Jim has the answer: c(0.5, nc+0.5) and
0.5 + c(0, nc) are identical.

I think the problem is this call within heatmap():

    image(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + 
        c(0, nr), axes = FALSE, xlab = "", ylab = "", ...)

So, if you put a `ylim` in your ... argument, the above call has two
ylim arguments.

Edit your own copy of myheatmap <- fix(heatmap); put
xlim = NULL, ylim = NULL in the arguments to
the myheatmap function, change the image call to state

xlim = if (is.null(xlim)) 0.5 + c(0, nc) else xlim,
ylim = if (is.null(ylim)) 0.5 + c(0, nc) else ylim,

and then you can specify a ylim or not, as required.

WARNING: THE ABOVE CODE IS NOT TESTED

Simon

PS it is always good to read `heatmap` as well as `?heatmap`!

> -----Original Message-----
> From: James MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: 05 January 2004 13:35
> To: johanl at kiev.biotech.kth.se; r-help at stat.math.ethz.ch
> Subject: Re: [R] Analyzing dendograms??
> 
> 
> Security Warning: 
> If you are not sure an attachment is safe to open please contact  
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> ________________________________________________________________ 
>  
> You are using the xlim and ylim arguments incorrectly. You 
> should be doing something like xlim=c(0.5, nc+0.5), 
> ylim=c(0.5, nc+0.5). The error message gave you this hint.
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> Johan Lindberg <johanl at kiev.biotech.kth.se> 01/05/04 06:19AM >>>
> Thanks for the ideas but I already tested to give the 
> heatmapfunction the 
> argument ylim but I get the following error message:
> 
> Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), 
> ylim = 0.5 +  :
>          formal argument "ylim" matched by multiple actual arguments
> 
> So then I tried to adjust the function and changed the ylim 
> argument when 
> the "heatmapfunction" calls "image". But this only makes it 
> possible to 
> zoom in on the "picture" that is drawn in the 
> heatmapfunction. The result 
> is that the function draws the full dendogram on a truncated picure.
> 
> Any ideas, anyone?
> 
> / Johan
> 
> 
> At 13:31 2004-01-04 -0500, you wrote:
> >Johan  -
> >
> >Disclaimer:  I've never used  heatmap(), so probably I shouldn't
> >be answering this.
> >
> >However ... the function  heatmap() probably calls either  plot()
> >or  image() (regular graphics) or  xyplot() (lattice graphics)  in
> >order to set up axes and initialize the actual plotting.  heatmap()
> >may also have a  "..."  argument which passes additional parameters
> >through to  plot(), unchanged.  If both of my guesses are correct
> >(use  help("heatmap")  to find out) then I would try calling
> >heatmap() again with an additional parameter  ylim=c(a,b),  where
> >"a" and "b" are two numbers, with  a < b,  which indicate plotting
> >coordinates which bracket the group of genes you wish to zoom in on.
> >
> >It will take a bit of experimentation to figure out what internal
> >coordinate system  heatmap()  uses to do the plotting, but this
> >seems like a direct way to zoom in on just a part of the plot.
> >
> >This is completely untested.  I leave it to you to read  
> help("heatmap")
> >and see whether any of this makes sense.  Hope this helps.
> >
> >-  tom blackwell  -  u michigan medical school  -  ann arbor  -
> >
> >On Sun, 4 Jan 2004, Johan Lindberg wrote:
> >
> > >
> > > I have used heatmap to visualize my microarray data. I 
> have a matrix of
> > > M-values. I do the following.
> > >
> > > #The distance between the columns.
> > > sampdist <- dist(t(matrix[,]), method="euclidean")
> > > sclus <- hclust(sampdist, method="average")
> > > #The distance between the rows.
> > > genedist <- dist(matrix[,], method="euclidean")
> > > gclus <- hclust(genedist, method="average")
> > > 
> heatmap(matrix[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram
> (sclus), 
> > col=rbg)
> > >
> > > So far so good. But what if I want to look at a group of 
> genes that appear
> > > to have the same expression pattern in the heatmap? How 
> do I zoom in on a
> > > dendogram in a heatmap to look at which genes that are forming the
> > > interesting clusters? I would really appreciate if 
> someone could give me a
> > > pointer.
> > >
> > > Best regards.
> > >
> > > / Johan
> > >
> > >
> > >
> > > 
> > 
> **************************************************************
> *****************************
> > > Johan Lindberg
> > > Royal Institute of Technology
> > > AlbaNova University Center
> > > Stockholm Center for Physics, Astronomy and Biotechnology
> > > Department of Molecular Biotechnology
> > > 106 91 Stockholm, Sweden
> > >
> > > Phone (office): +46 8 553 783 45
> > > Fax: + 46 8 553 784 81
> > > Visiting adress: Roslagstullsbacken 21, Floor 3
> > > Delivery adress: Roslagsvägen 30B
> > >
> > > ______________________________________________
> > > R-help at stat.math.ethz.ch mailing list
> > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help 
> > >
> 
> **************************************************************
> *****************************
> Johan Lindberg
> Royal Institute of Technology
> AlbaNova University Center
> Stockholm Center for Physics, Astronomy and Biotechnology
> Department of Molecular Biotechnology
> 106 91 Stockholm, Sweden
> 
> Phone (office): +46 8 553 783 45
> Fax: + 46 8 553 784 81
> Visiting adress: Roslagstullsbacken 21, Floor 3
> Delivery adress: Roslagsvägen 30B
> 
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Simon Fear 
Senior Statistician 
Syne qua non Ltd 
Tel: +44 (0) 1379 644449 
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email: Simon.Fear at synequanon.com 
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