It seems as if, Rowv and Colv are dendrograms. I've pasted my exact commands and errors below. With heatmap I get a nice heatmap and dendograms, but with heatmap.2 it omits the dendograms. I guess I"ll just forget about it, and just re-compute the dendrograms each time I use heatmap.2. I wish heatmap had a key. > Rowv 'dendrogram' with 2 branches and 2913 members total, at height 17.27877 > Colv 'dendrogram' with 2 branches and 6 members total, at height 209.7754 > heatmap(myma,Rowv=Rowv,Colv=Colv) > heatmap.2(myma,Rowv=Rowv,Colv=Colv) Warning messages: 1: Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram. in: heatmap.2(myma, Rowv = Rowv, Colv = Colv) 2: Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column dendogram. in: heatmap.2(myma, Rowv = Rowv, Colv = Colv) > -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Friday, December 14, 2007 3:42 PM To: alison waller Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Extracting dendogram information from Heatmaps Are you sure that your Rowv is a dendrogram? This works for me: > dat <- matrix(rnorm(1000), ncol=10) > Rowv <- as.dendrogram(hclust(dist(dat))) > Colv <- as.dendrogram(hclust(dist(t(dat)))) > heatmap.2(dat, Rowv=Rowv, Colv=Colv) Best, Jim alison waller wrote: > No, it doesn't appear as if the matrix is mixed up the rows are equal in > length. > > Interestingly, I can use Rowv=Rowv and Colv=Colv with the heatmap command > successfully, but not with the heatmap.2 command. > > > -----Original Message----- > From: 'Thomas Girke' [mailto:thomas.girke at ucr.edu] > Sent: Friday, December 14, 2007 12:52 AM > To: alison waller > Cc: 'James W. MacDonald'; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Extracting dendogram information from Heatmaps > > You may have mixed up the orientation of your matrix. Does > length(myclust$labels) correspond to the number of rows in > myma? > > Thomas > > On Fri 12/14/07 00:05, alison waller wrote: >> Great, I passed genes names to the matrix through rownames(myma). >> >> Your example below is great! >> >> However, I would like to use heatmap.2 and am having trouble specifying > the >> Row clustering. I made Rowv and Colv, >> Rowv=as.dendrogram(myclust),Colv<-as.dendrogram(hclust(dist(t(myma) ))). > And >> thought I could just create the heatmap as below. >> But it won't let me pass it Rowv or Colv, so the computer has to > recalculate >> the clusters everytime I want to change colors or something little (this >> takes a while). Is there something wrong with my syntax? >> >> >> >> heatmap.2(myma,Rowv=Rowv,Colv=Colv,col=topo.colors(75),RowSideColors=m ycolh >> c42,trace='none',labRow=FALSE,key=T) >> Warning messages: >> 1: gamma cannot be modified on this device >> 2: Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row >> dendogram. in: heatmap.2(myma, Rowv = Rowv, Colv = Colv, col = >> topo.colors(75), >> 3: Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column >> dendogram. in: heatmap.2(myma, Rowv = Rowv, Colv = Colv, col = >> topo.colors(75), >> >> heatmap.2(myma,Rowv=Rowv,col=topo.colors(75),RowSideColors=mycolhc42,t race= >> 'none',labRow=FALSE,key=T) >> Warning message: >> Discrepancy: Rowv is FALSE, while dendrogram is `column'. Omitting row >> dendogram. in: heatmap.2(myma, Rowv = Rowv, col = topo.colors(75), >> RowSideColors = mycolhc42, >>> ?heatmap.2 >> -----Original Message----- >> From: 'Thomas Girke' [mailto:thomas.girke at ucr.edu] >> Sent: Thursday, December 13, 2007 1:21 PM >> To: alison waller >> Cc: 'James W. MacDonald'; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Extracting dendogram information from Heatmaps >> >> The best way to answer these questions is to subset your data set to >> to a test matrix with only a few rows. This way you can see the labels >> in the plot and things become intuitive. >> For example: >> myma <- MA$M[fitp,] >> myma <- myma[1:20,] >> >> Row names can always be assigned by you with >> rownames(myma) <- mynames >> >> If your data set has a label column, then it would be >> rownames(myma) <- myname$label >> >> To be sure your data set is a matrix, you do: >> myma <- as.matrix(myma) >> >> Continue with hclust ... >> >> Thomas >> >> On Thu 12/13/07 12:50, alison waller wrote: >>> Thanks everyone, these are great suggestions. >>> >>> I had trouble with the identify, as the plot moved when I clicked the >> mouse >>> and I got error messages. >>> >>> The cutree worked well - however, I see a matrix which has values >>> corresponding to clusters, but is cluster one the leftmost or rightmost >>> cluster? Ie. how are they ordered. >>> >>> The $labels method seems the best but my matrix doesn't seem to have >> labels. >>> I made my matrix from the M values from an MAList, is there a way to > carry >>> through the gene names? >>> >>> Myclust<-hclust(dist(MA$M[fitp,]) >>> Myclust$labels gives NULL >>> >>> Thanks again, >>> >>> alison >>> >>> >>> -----Original Message----- >>> From: Thomas Girke [mailto:thomas.girke at ucr.edu] >>> Sent: Thursday, December 13, 2007 12:00 PM >>> To: James W. MacDonald >>> Cc: alison waller; bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] Extracting dendogram information from Heatmaps >>> >>> Alison, >>> >>> In addition to James' suggestions, you may want to get familiar how to >>> access the >>> different data components of the resulting hclust object (e.g. labels, >>> order) and >>> the cutree() function. If you can't read the labels in the plots, then > you >>> can >>> always extract them in clean text in the corresponding tree order (see >>> below: >>> hr$labels[hr$order]) from the hclust objects. >>> >>> Here is a short example to illustrate a possible > hclust-heatmap/heatmap.2 >>> routine: >>> >>> # Generate a sample matrix >>> y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), >>> paste("t", 1:5, sep=""))) >>> >>> # Cluster rows and columns by correlation distance >>> hr <- hclust(as.dist(1-cor(t(y), method="pearson"))) >>> hc <- hclust(as.dist(1-cor(y, method="spearman"))) >>> >>> # Obtain discrete clusters with cutree >>> mycl <- cutree(hr, h=max(hr$height)/1.5) >>> >>> # Prints the row labels in the order they appear in the tree. >>> hr$labels[hr$order] . >>> # Prints the row labels and cluster assignments >>> sort(mycl) >>> >>> # Some color selection steps >>> mycolhc <- sample(rainbow(256)) >>> mycolhc <- mycolhc[as.vector(mycl)] >>> >>> # Plot the data matrix as heatmap and the cluster results as dendrograms >>> with heatmap or heatmap.2 >>> # and show the cutree() results in color bar. >>> heatmap(y, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), scale="row", >>> RowSideColors=mycolhc) >>> >>> library("gplots") >>> heatmap.2(y, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), >>> col=redgreen(75), scale="row", >>> ColSideColors=heat.colors(length(hc$labels)), RowSideColors=mycolhc, >>> trace="none", key=T, cellnote=round(t(scale(t(y))),1)) >>> >>> >>> Best, >>> Thomas >>> >>> On Thu 12/13/07 09:58, James W. MacDonald wrote: >>>> Hi Alison, >>>> >>>> alison waller wrote: >>>>> Hello Everyone, >>>>> >>>>> >>>>> >>>>> I've been using heatmap and heatmap.2 to draw heatmaps for my >>> experiments. >>>>> >>>>> >>>>> I have a heatmap of the M values of 6 arrays for the spots with >> pvalues >>> were >>>>> <0.005 (from eBayes). >>>>> >>>>> However, I would like to see which spots it has grouped together in >> the >>> row >>>>> dendogram. Is there a way I can extract the information about the >> spots >>>>> that are clustered together. I cannot read the row names, and even > if >> I >>>>> could I was hoping there would be some way to list the clusters and >> save >>> it >>>>> to a file. >>>> There are two ways to do this that I know of. And either can be a > pain, >>>> depending on how big the dendrogram is. >>>> >>>> Both methods require you to construct your dendrogram first. You can >>>> then choose the clusters with the mouse. This might be more difficult > if >>>> you have some gigantic dendrogram and have ingested too much coffee > ;-D. >>>> Normally, one would simply do >>>> >>>> heatmap(mymatrix, otherargs) >>>> >>>> and accept the default clustering method. However, you can always >>>> pre-construct the dendrograms and then feed those to heatmap(). >>>> >>>> Rowv <- as.dendrogram(hclust(dist(mymatrix))) >>>> Colv <- as.dendrogram(hclust(dist(t(mymatrix)))) >>>> >>>> heatmap(mymatrix, Rowv=Rowv, Colv=Colv, otherargs) >>>> >>>> Now if you do something like that, then you can try >>>> >>>> plot(Rowv) >>>> a.cluster <- identify(Rowv) >>>> >>>> and then use your mouse to choose the upper left corner of a rectangle > >>>> that encompasses the cluster you are interested in. Here is where the >>>> size of the dendrogram and the amount of coffee comes in. If the >>>> dendrogram is really large then identify() may not be able to figure > out >>>> what you are trying to select, or may decide you are choosing the > upper >>>> right corner. >>>> >>>> You can choose as many clusters as you want, and they will be in the >>>> list a.cluster, in the order you selected. >>>> >>>> A more programmatic method is to use rect.hclust() and either choose > the >>>> height at which to make the cuts, or the number of clusters, etc. > Again, >>>> depending on the size of your dendrogram, this may work well or it may > >>>> be painful. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> >>>>> Alison >>>>> >>>>> >>>>> >>>>> ****************************************** >>>>> Alison S. Waller M.A.Sc. >>>>> Doctoral Candidate >>>>> awaller at chem-eng.utoronto.ca >>>>> 416-978-4222 (lab) >>>>> Department of Chemical Engineering >>>>> Wallberg Building >>>>> 200 College st. >>>>> Toronto, ON >>>>> M5S 3E5 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> Affymetrix and cDNA Microarray Core >>>> University of Michigan Cancer Center >>>> 1500 E. Medical Center Drive >>>> 7410 CCGC >>>> Ann Arbor MI 48109 >>>> 734-647-5623 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> -- >>> Thomas Girke >>> Assistant Professor of Bioinformatics >>> Director, IIGB Bioinformatic Facility >>> Center for Plant Cell Biology (CEPCEB) >>> Institute for Integrative Genome Biology (IIGB) >>> Department of Botany and Plant Sciences >>> 1008 Noel T. Keen Hall >>> University of California >>> Riverside, CA 92521 >>> >>> E-mail: thomas.girke at ucr.edu >>> Website: http://faculty.ucr.edu/~tgirke >>> Ph: 951-827-2469 >>> Fax: 951-827-4437 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> Thomas Girke >> Assistant Professor of Bioinformatics >> Director, IIGB Bioinformatic Facility >> Center for Plant Cell Biology (CEPCEB) >> Institute for Integrative Genome Biology (IIGB) >> Department of Botany and Plant Sciences >> 1008 Noel T. Keen Hall >> University of California >> Riverside, CA 92521 >> >> E-mail: thomas.girke at ucr.edu >> Website: http://faculty.ucr.edu/~tgirke >> Ph: 951-827-2469 >> Fax: 951-827-4437 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623