search for: cexrow

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 t...

...uot;,"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 anyone let me...

Hi, I would like to change the font type (to courier) of my rows labels when I plot a heatmap with R. I have used cexRow=0.7 to modify the size but didn't find anything regarding font type. heatmap(as.matrix(cebpa50), margins=c(5,10) , Colv=NA , scale="column", col=col4, cexRow=0.7) Thanks, Ben

...#39;,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 realizarse con la...

...on 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

...rary("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...

...> library("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...

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...

...] 6 105 0 0 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 (1,5...

...# generate 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

...olv=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_64 os darwin13...

...s and spend 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...

...ead.table("chitekete.csv", header = T, row.names=1, sep=","); xcc <- cor(zcz); pdf("SIGA.pdf", height=10,width=9) heatmap.2(xcc, margins= c(9,9), col = bluered(64), trace=c("none"), breaks=c(seq(-1,1,1/32)), symkey=TRUE, density.info="histogram", cexRow=1) I thank you all. Paul -- BEST Paul Murima

...bounds and doesn'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_...

...a[,2:5] heatdata_matrix <- data.matrix(heatdata) rownames(heatdata_matrix) = paste("Gene", 2:655) x11() data_heatmap <- heatmap.2(heatdata_matrix, col=redblue(75), scale="row", key=TRUE, symkey=FALSE, density.info="none", trace="none", margins=c(10,10), cexRow=0.5) jpeg("Heatmap_bin17.jpeg", width=8, height=8, units="in", res=300, quality=100) The heat map looks like this (with red green coloring): <http://r.789695.n4.nabble.com/file/n4648806/Heatmap_bin20.jpeg> I fixed the margin issues (not seen in image), but I would like...

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://phylotemp.microeco.o...

...uot;, "PTH", "IGFBP2", "OPG", "IL1Ra", "TNFA"))) heatmap.2(abnr, breaks=c(0,0.05,0.1,0.25,0.35), col=brewer.pal(4,"Blues"), Rowv=FALSE, Colv=FALSE,symm=TRUE, key=TRUE,symkey=FALSE, density.info="none", trace="none", cexRow=0.75, keysize=0.8, scale = "none", dendrogram="none",main='AbN') I would appreciate any response on this. Thanks sharad -- View this message in context: http://r.789695.n4.nabble.com/labeling-rows-in-heatmap-2-tp4490314p4490314.html Sent from the R help mailing lis...

...", # 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", # superimpose "histogram" or a...

...eaks = 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" "density.info" [17] &qu...

...lse 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(), one might expect also user-supplied labels to be re-ordered together with the rows and...