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:[EMAIL PROTECTED] > Sent: 05 January 2004 13:35 > To: [EMAIL PROTECTED]; [EMAIL PROTECTED] > Subject: Re: [R] Analyzing dendograms?? > > > Security Warning: > If you are not sure an attachment is safe to open please contact > Andy on x234. There are 0 attachments with this message. > ________________________________________________________________ > > 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 <[EMAIL PROTECTED]> 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 > > > > > > ______________________________________________ > > > [EMAIL PROTECTED] 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 > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Simon Fear Senior Statistician Syne qua non Ltd Tel: +44 (0) 1379 644449 Fax: +44 (0) 1379 644445 email: [EMAIL PROTECTED] web: http://www.synequanon.com Number of attachments included with this message: 0 This message (and any associated files) is confidential and\...{{dropped}} ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html