>X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 >Date: Thu, 27 Nov 2003 08:12:22 +0100 >To: Marcus <marcusb@biotech.kth.se> >From: Johan Lindberg <johanl@kiev.biotech.kth.se> >Subject: Re: Fwd: Re: [BioC] Clustering in R.... >X-MIME-Autoconverted: from quoted-printable to 8bit by kiev.biotech.kth.se >id hAR7HNPr006352 > >That did the trick ! >Thank you Sean for the help. > >Now I have some more questions. I read a tutorial on the webb that didnt >include any R code that it was possible to identify in a Heatmap which >genes that are in specific clusters. In other programs such as GeneSpring >you could just click on the dendogram to get a list of the genes of >interest. How do one perform such an operation in R? Is it possible? I >mean, is the heatmap only for visualization or can one look at the >different clustered groups in some way? > >And a question about levelplot. When you plot the correlation with >levelplot you do not get the names of your samples on either the x or the >y axis. In a plot like barplot it works with the argument >names.arg=namevector but I havent found anything like that for levelplot. >A tip anyone? > >Cheers > >/Marcus > > >At 10:09 2003-11-12 +0100, you wrote: > >>>User-Agent: Microsoft-Entourage/10.0.0.1309 >>>Date: Tue, 11 Nov 2003 06:33:22 -0500 >>>Subject: Re: [BioC] Clustering in R.... >>>From: Sean Davis <sdavis2@mail.nih.gov> >>>To: Marcus <marcusb@biotech.kth.se> >>>X-MIME-Autoconverted: from quoted-printable to 8bit by >>>kiev.biotech.kth.se id hABBWFPr030178 >>> >>>Marcus, >>> >>>Here is a fairly general method for working with heatmap that I have used. >>>You can substitute any function that you want for distance (eg., >>>1-correlation, etc.) and for clustering (don't have to use hclust). Make >>>sure that you do the coercion (to distance or dendrogram objects as needed), >>>though. Also, some distance functions that you can dream up will not work >>>with NA's, but dist does. >>> >>> > m <- matrix(rnorm(100),nrow=10,ncol=10) >>> > m >>> [,1] [,2] [,3] [,4] [,5] [,6] >>> [1,] -1.0326191 1.09744204 0.9923254 -0.05780237 1.6853566 -0.5938021 >>> [2,] -0.6493561 -0.58846041 0.8735639 0.34492342 -0.1398261 1.4288108 >>> [3,] -1.0020073 0.75130128 -2.6110435 1.27265445 0.1211387 0.7048981 >>> [4,] -0.1658810 0.45351434 -0.8973168 -0.17738084 -0.1056792 -1.7251339 >>> [5,] 0.1466563 0.11917823 0.9372353 0.29040600 0.8463049 0.9192848 >>> [6,] 0.6020565 -0.90338771 -0.7453363 -1.34284821 -0.7684490 0.2177409 >>> [7,] 0.5290555 0.58798246 0.4085396 0.63305003 0.2014624 -0.5613248 >>> [8,] 1.4456958 0.06372875 0.1829127 0.20681971 0.5745696 -0.3555856 >>> [9,] 0.5973093 -0.35483585 1.1074023 0.63930734 -1.2452399 -1.2721422 >>>[10,] 1.2563169 0.92249574 -0.7103717 -0.41067056 0.2277188 0.3861969 >>> [,7] [,8] [,9] [,10] >>> [1,] -1.63852314 -1.0773165 0.5601368 1.05115476 >>> [2,] -0.14026278 -0.9013605 0.1581475 0.36730440 >>> [3,] 0.45517561 -1.5211124 -1.1641732 1.97321531 >>> [4,] 0.08338336 1.4846938 0.3096862 0.44513675 >>> [5,] 0.85917332 1.0337033 -0.1784938 -0.48848017 >>> [6,] 0.05054810 1.3712665 -0.6545246 0.10251154 >>> [7,] 2.30894410 -0.6089214 1.5761573 0.66912925 >>> [8,] -0.85946317 0.0855971 -0.7014037 -2.19050881 >>> [9,] 1.53911617 1.1185075 0.2428764 -0.09556405 >>>[10,] -1.61446618 1.0605298 0.5160358 0.04152571 >>> > m[10,1:8] <- NA >>> > m >>> [,1] [,2] [,3] [,4] [,5] [,6] >>> [1,] -1.0326191 1.09744204 0.9923254 -0.05780237 1.6853566 -0.5938021 >>> [2,] -0.6493561 -0.58846041 0.8735639 0.34492342 -0.1398261 1.4288108 >>> [3,] -1.0020073 0.75130128 -2.6110435 1.27265445 0.1211387 0.7048981 >>> [4,] -0.1658810 0.45351434 -0.8973168 -0.17738084 -0.1056792 -1.7251339 >>> [5,] 0.1466563 0.11917823 0.9372353 0.29040600 0.8463049 0.9192848 >>> [6,] 0.6020565 -0.90338771 -0.7453363 -1.34284821 -0.7684490 0.2177409 >>> [7,] 0.5290555 0.58798246 0.4085396 0.63305003 0.2014624 -0.5613248 >>> [8,] 1.4456958 0.06372875 0.1829127 0.20681971 0.5745696 -0.3555856 >>> [9,] 0.5973093 -0.35483585 1.1074023 0.63930734 -1.2452399 -1.2721422 >>>[10,] NA NA NA NA NA NA >>> [,7] [,8] [,9] [,10] >>> [1,] -1.63852314 -1.0773165 0.5601368 1.05115476 >>> [2,] -0.14026278 -0.9013605 0.1581475 0.36730440 >>> [3,] 0.45517561 -1.5211124 -1.1641732 1.97321531 >>> [4,] 0.08338336 1.4846938 0.3096862 0.44513675 >>> [5,] 0.85917332 1.0337033 -0.1784938 -0.48848017 >>> [6,] 0.05054810 1.3712665 -0.6545246 0.10251154 >>> [7,] 2.30894410 -0.6089214 1.5761573 0.66912925 >>> [8,] -0.85946317 0.0855971 -0.7014037 -2.19050881 >>> [9,] 1.53911617 1.1185075 0.2428764 -0.09556405 >>>[10,] NA NA 0.5160358 0.04152571 >>> > sampdist=dist(t(m)) >>> > sclus=hclust(sampdist) # sclus is a dendrogram that you can plot(sclus) >>> > genedist=dist(m) >>> > gclus=hclust(genedist) # gclus is also a dendrogram >>> > heatmap(m,Rowv=gclus,Colv=sclus) #this doesn't work! >>>Error in lV + rV : non-numeric argument to binary operator >>> > heatmap(m,Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus)) # need >>> proper >>>coercion for this to work >>> >>>Although this works, note that using a gene that has 16 NA values out of 22 >>>is probably not going to be useful, as the distance matrix for this example >>>for the genes is: >>> >>> > genedist >>> 1 2 3 4 5 6 7 8 >>>2 3.673241 >>>3 5.235695 4.536603 >>>4 4.381494 4.522069 5.046200 >>>5 4.367649 2.821795 5.437622 3.688942 >>>6 5.408318 3.863713 5.380546 3.014530 3.345877 >>>7 4.764409 3.915998 5.194822 3.911820 3.548220 4.830247 >>>8 4.825510 4.216357 6.212646 4.149383 3.314914 3.844966 5.041345 >>>9 5.536079 4.169987 6.179576 3.158424 3.249127 3.637840 3.149486 4.264858 >>>10 2.259752 1.082164 5.724739 1.013612 1.953558 2.621002 2.754763 5.685128 >>> 9 >>>2 >>>3 >>>4 >>>5 >>>6 >>>7 >>>8 >>>9 >>>10 0.6834093 >>> >>>See how much different the distance involving row 10 is from the others--the >>>NA values were simply dropped. You will probably have to either deal with >>>the missing values beforehand or use another distance measure that is not >>>sensitive to NA values. I can't tell you what to do on that part, as that >>>is also somewhat dependent on your need to use that gene and the >>>practicality of doing more experiments. >>> >>>Let me know if that helps. >>> >>>Sean >>> >>> >>>On 11/10/03 7:41 AM, "Marcus" <marcusb@biotech.kth.se> wrote: >>> >>> > >>> > >>> >> Hello again. Back from some weeks of laborative work I still have some >>> >> questions on clustering in R. >>> >> >>> >> I got a lot of help from Sean Davis (thanks a lot :o) ) so if he or >>> >> someone else have the time.... >>> >> >>> >> My problem is that I have some spots flagges as NA in a matrix of >>> M-values >>> >> organised slidewise. I want to cluster those but I get error >>> messages when >>> >> using heatmap due to the NA:s in the matrix. I mailed Andy Liaw (who >>> wrote >>> >> the heatmap function) and he gave med the tip to look into the daisy >>> >> function. And the daisy function is supposed to handle NA:s. >>> >> >>> >> But what do you get out of the function? >>> >> >>> >> test <- daisy(mymatrix) >>> >> This creates an object of type dissimilarity right? And you can >>> convert it >>> >> into a matrix with the help of >>> >> testII <- as.matrix(test) >>> >> Is this what I should use hclust on? or should I do >>> >> testIII <- as.dist(testII) before. Neither works so I do not know really >>> >> what is true. >>> >> >>> >> And I tried to use daisy directly with heatmap but that didnt work but >>> >> produced the same error as with dist. >>> >> >>> >> heatmap(mymatrix[1:22,], distfun = dist) >>> >> Error in hclustfun(distfun(x)) : NA/NaN/Inf in foreign function call >>> (arg 11) >>> >> This is due to the fact that I only have 2 M-values in the twentisecond >>> >> row and 16 NA:s. >>> >> >>> >> So basically my question is, how do you do to get heatmap to work with a >>> >> matrix of M-values that has got spots flagged NA in them ? What distance >>> >> function works and how do you use it? >>> >> >>> >> Could someone please help me and perhaps write an example of how to >>> do. I >>> >> think the help files are not so good in this perspective. >>> >> >>> >> Best regards >>> >> >>> >> / Marcus >>> > >>> > >>> ****************************************************************** ************ >>> > ************* >>> > Marcus Gry Bj?rklund >>> > >>> > 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: Roslagsv?gen 30B >>> > >>> > _______________________________________________ >>> > Bioconductor mailing list >>> > Bioconductor@stat.math.ethz.ch >>> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >>> > >> >>******************************************************************** *********************** >>Marcus Gry Bj?rklund >> >>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: Roslagsv?gen 30B >>******************************************************************** *********************** >> > >********************************************************************* ********************** >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: Roslagsv?gen 30B >********************************************************************* ********************** > > ********************************************************************** ********************* Marcus Gry Bj?rklund 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: Roslagsv?gen 30B