search for: cexcol

...quot;red","yellow","darkgreen"),space="Lab", bias=1.5) heatmap.2(matrix, Colv=1:ncol(matrix), dendogram="row", hclustfun=function(m) hclust(m,method="complete"),col=cp(25),scale="none",trace="none",keysize=1,margins=c(5,12), cexCol=1, cexRow=1) q() dev.off() The alternative that i tried to avoid the reordering was heatmap.2(matrix, Rowv=NULL, Colv=NULL, col=cp(25), scale="none", trace="none", keysize=1, margins=c(5,12), cexCol=1, cexRow=1) But the above command doesnt generate the heatmap. So could any...

...ersion 2.9.0 (2009-04-17) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 # The correct results > hv <- heatmap.2(x, col=col.palette, Colv=FALSE, key=TRUE, Rowv=cc1$order, dendrogram="row", scale="none", tracecol="white", cexCol=.5) > hv$rowInd [1] 26 23 5 19 15 4 2 16 21 13 22 12 10 20 7 3 25 1 8 11 24 9 18 14 17 [26] 6 # Attempt 1 > cc = as.dendrogram(hclust(dist(x))) > hv1 <- heatmap.2(x, col=col.palette, Rowv=cc, Colv=FALSE, key=TRUE, dendrogram="row", scale="none", tr...

...M10A'',1:30,sep="") colnames(x) <- paste(''Muestra_'',1:8,sep="") # Mapa require(gplots) heatmap.2(x, key=TRUE, symkey=TRUE, keysize = 0.9, col= rev(heat.colors(30)), density.info="none", trace="none", cexCol=1, cexRow=.7, xlab=''Muestra'') Cómo podrán ver, en la parte superior izquierda hay un recuadro con los textos "Color Key" y "Value". Alguien sabe cómo eliminarlos? Muchas gracias por su ayuda, Jorge Ivan Velez PS: No necesariamente el heatmap debe realiza...

...sion: Version 1.8.1 OS: Irix64 Submission from: (NULL) (130.225.67.236) I've made a script look like this: exp <- read.table("graph/1933672048.cluster.data") exp <- as.matrix(exp) postscript("graph/1933672048.cluster.data.ps") heatmap(exp,scale="none",cexCol=0.4,cexRow=0.2,col=custom,margins=c(5,5)) The row labels on the output PostScript file are skewed vertically downwards - in fact more than the height of 2 rows! I have roughly 200 rows and 4 columns in my dataset. It is therefor very difficult to see which label goes to which row

...vgDevice") > jpeg("Heatmap.jpg", height=6+2/3, width=6+2/3, units="in", res=1200) > heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), > dendrogram="both", scale="row", col=brewer.pal(3, "YlOrRd"), cexRow=0.01, cexCol=0.01, trace="none", density.info="none", key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) > dev.off() I would like to save the file in a graphical format that can be edited later in any image editing program (like corel). is there a way...

...("RSvgDevice") > jpeg("Heatmap.jpg", height=6+2/3, width=6+2/3, units="in", res=1200) > heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), dendrogram="both", scale="row", col=brewer.pal(3, "YlOrRd"), cexRow=0.01, cexCol=0.01, trace="none", density.info="none", key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) > dev.off() I would like to save the file in a graphical format that can be edited later in any image editing program (like corel). is there a way...

Hello, I have a large (919 X 919), hierarchically clustered heatmap that I would like to read the labels off of. I have tried saving the figure in pdf format and enlarging it until I can see the labels, but if I make the labels small enough to read (so that they don't overlap) using cexRow and cexCol, they do not appear in the pdf. The limit seems to be anything below cexRow or Col = 0.06. Is there a way to have smaller labels visible in the pdf? Is this an issue with resolution? I could get by with just a quarter of the heatmap (i.e. half of a row and half of a column) so that the labels d...

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how to export the column clustering dendrogram out. Because I want to get the dendrogram for next step analysis. If I can export it as the newick format (or nexus forma...

...6 and call: ##------------ Heatmap -------------- library(RColorBrewer) rc <- grey((nrow(x):1)/nrow(x)) heatmap(data.matrix(x[,1:4]), Rowv=NA, Colv=NA, scale='none',labCol=NULL, revC=TRUE, col = brewer.pal(9,'Greys'), ylab='time',margins=c(6,5), cexRow=1.5, cexCol=1.5, RowSideColors = rc) I end up with something like attached 'heatmap'. How can I change my call to: 1) most important: there are black strips on the right-hand side, these are the row numbers packed one on another. How to put there time points over, say, 500 sec epochs (1,500, 1000...)...

...nerate heat map library(gplots) if (is.null(sample_output)) { pdf( "Heatmap.pdf") } else { pdf(file=paste("Heatmap_", sample_output, ".pdf", sep="")) } heatmap.2(as.matrix(my.dataM),Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc),cexRow=0.01, cexCol=0.8, dendrogram="none", col=greenred(100), scale="row",key=TRUE, trace="none",density.info="none", symkey=FALSE, main=paste("Heatmap_", sample_output)) dev.off() -------------- Thanks, Dorothy

...trace="none",Colv=FALSE, dendrogram = "none", density.info="none", key="TRUE", keysize = 2, key.xlab = "Log2FC", key.title = "key", cexCol=3.0, cexRow=2, lwid= c(0.4,1), lhei = c(0.1, 4), margins= c(50,80), symm=F,symkey=F,symbreaks=T, scale="none") dev.off() > R.version _ platform x86_64-apple-darwin13.4.0 arch x86...

...several hours with trial and error, but didn't find a correct way. It's all about lines in a heatmap to separate different data block from each other to underline the significance of the found clusters! The heatmap is build like that: heatmap(X, Rowv=NA, Colv=NA, symm=TRUE, cexRow=0.3, cexCol=0.3) I switched the dendrograms off, because I don't want the values sorted but in the way, I extracted them from the data. I tried to enter the lines that way: lines(c(14,14),c(0,187), col="green") That should appear as a line parallel to the x-axis, but there was no line at al...

...t show up. I am outputting to pdf. Any help? Thanks, Mark heatmap(x = dataM, RowSideColors = RowSideColors, ColSideColors=ColSideColors, main = title, margins = c(50,50), scale= do.scale ,labRow=geneNames, labCol=colLabels, col = hmcol, cex.main = 1, cexRow = row.lab.mag, cexCol = col.lab.mag) > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-29 r42686) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC...

...drogram while seeing the labels. I would like to try to have a tall, skinny heatmap with row labels big enough to read. I was able to get closer to what I want with this command... jpeg(file = "view_heat.jpg",width = 4000, height = 6000) heatmap(elmat,col= brewer.pal(9,"PuOr"), cexCol = .8, margin = c(.01,130)) # dev.off() but it only uses a quarter of the jpeg and it is still really hard to see both the dendrogram on the left and read the labels on the right. Is there a way I can set the actual width and height of the cells so I can use the full size of the jpeg and read my la...

...drogram while seeing the labels. I would like to try to have a tall, skinny heatmap with row labels big enough to read. I was able to get closer to what I want with this command... jpeg(file = "view_heat.jpg",width = 4000, height = 6000) heatmap(elmat,col= brewer.pal(9,"PuOr"), cexCol = .8, margin = c(.01,130)) # dev.off() but it only uses a quarter of the jpeg and it is still really hard to see both the dendrogram on the left and read the labels on the right. Is there a way I can set the actual width and height of the cells so I can use the full size of the jpeg and read my la...

Hi Chakravarthy, [dont forget to Cc the list for useRs with the same Q.] If you're trying to reuduce the isze of your row or column labels, i think the following arguments of heatmap.2 {gplots} is what you want to adjust- 'cexCol' and 'cexRow'. Specifically on my question that you ask about, i found the BioC forum helpful: http://permalink.gmane.org/gmane.science.biology.informatics.conductor/30112 And in fact the phylotemp() function by default pretty much did exactly what i needed, available here: http:/...

...# reorder dendrogram dendrogram="both", # dendrograms to draw col=pal, # palette (see above) trace="none", # trace line (show distance) cexCol=cex_val, # size of column labels cexRow=cex_val, # size of row labels key=TRUE, # show the colour key keysize=cex_val, # key size density.info="none&...

...ncol = 1), col = col, breaks = tmpbreaks, xaxt Selection: 2 Called from: eval(expr, envir, enclos) Browse[1]> heatmap.func.R Error during wrapup: object 'heatmap.func.R' not found Browse[1]> ls() [1] "add.expr" "breaks" "cellnote" "cexCol" [5] "cexRow" "col" "colInd" "colsep" [9] "ColSideColors" "Colv" "ddc" "ddr" [13] "dendrogram" "densadj" "denscol" "den...

...(is.null(labRow)) labRow <- if (is.null(rownames(x))) (1:nr)[rowInd] else rownames(x) if (is.null(labCol)) labCol <- if (is.null(colnames(x))) (1:nc)[colInd] else colnames(x) ... axis(1, 1:nc, labels = labCol, las = 2, line = -0.5, tick = 0, cex.axis = cexCol) axis(4, iy, labels = labRow, las = 2, line = -0.5, tick = 0, cex.axis = cexRow) To see an example, try a <- matrix(c(1,1,1,2,0,2), nrow=3) rownames(a) <- 1:3 x11() heatmap(a) x11() heatmap(a, labRow=rownames(a)) Is this really meant to work like this? - From the help of heatmap()...

...r)]; mycolhc <- mycolhc[as.vector(myclhc)]; jpeg("scaleRow.jpg", height=6+2/3, width=6+2/3, units="in", res=1200) heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), dendrogram="both", scale="row", col=rev(heat.colors(10)), cexRow=0.08, cexCol=0.08, trace="none", density.info="none", symkey= FALSE, key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) dev.off() My question is, in the dataset I have good number of rows (~ 17) that has zero value for all the columns defined. So when I run t...