search for: greenr

Hi folks, I am wondering if the following is possible: I want to control the arguments sent to a function by string variables. For example, instead of > heatmap.2( A, col=greenred(75) ) I would want to have something like: > heatmap.2 ( paste(A, "col=greenred(75)", sep=",") ) Is this possible to do that? Thanks, D.

...like the 1st column of the matrix sorted from the highest to the lowest values - so that the colors reflected in the first column of the heatmap (top to bottom) go from red to green. After sorting the matrix (z), I tried the following command, but the data remains clustered. heatmap.2((z),col=greenred(100),dendrogram=NULL,Rowv=FALSE) I also tried the following, but the data remained clustered. heatmap.2((z),col=greenred(100),Colv=1:ncol(z)) ANY IDEAS?? Thanks so much, Peter

...going to look great... :-) What I'm out for, is to make green tones and red tones, and a relatively sharp break between them. This break will signify a rejection region for a test. I've spent all evening, er, night trying to tune this, but it's still ugly. My best shot so far is this: greenred <- palette(rgb(exp(-(0:255)/80), exp(-(0:255)/80), 0)) greenred2 <- greenred[c(1:160, 220:256)] and use greenred2. Any ideas...? Anybody got a pretty palette for this purpose? Also, I'd like to tune the palette so that the break between green and red happens at a value of e.g. 0.05. Ho...

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered. Either a 'dendrogram' or a vector of values used...

I'm working on some heatmaps, and the person I'm working with would prefer a red-black-green color palette (red denoting gene induction and green denoting gene repression). Does such a palette exist already? If not, is there an easy way to create one? Thanks, Jake

...0 times, but it's a 22kb file. completely use less !!! I really need to have high quality image, as I will have to work on photoshop and also I will have to cut and zoom in just some lines of my heatmap. #here is the code I use for my heatmap.2 : >heatmap.2(a_matrix, Rowv=NA, Colv =NA, col=greenred(60), scale="column", margins=c(7,10), trace="none", density.info=c("none")) Does someone know what I have to do in order to get my heatmap.2.png ??? Do I need some other package (I only use gplots, to allow the heatpmap.2) THANKS for your help Fred [[alternative...

Dear All: I tried to use heatmap.2 to generate hierarchical clustering using the following command: heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) datamatrix is subset of a RMA normalized data subset by a genelist. The problem is a lot of times, the z-score in key are from, like -5 to 15 or -15 to 5, as a result, the zero of z distribution are are either green region or r...

...I did. A2Rplot.hclust(hcc,k=length(num),col.up="black",col.down=num,lty.up=2,lty.down=1,lwd.up=1,lwd.down=2,show.labels=FALSE) #used the above external program to create a colored dendrogram xsort <- x[1:nrow(x), hcc$labels[hcc$order]] go<-genes[hc$order] image(scale(t(xsort)), col=greenred(60),xaxt="n", yaxt="n") di <- dim(x) nr<-di[1] nc<-di[2] axis(4, 1:nr, labels=go, las= 2, line= 0, tick=TRUE, cex.axis= 2) The output pdf I get is attached in this mail. I just get the first member of the vector "go" on axis(4). It looks like the program do...

...--------------------- library(gplots) mat <- matrix(sample(1:100,40),nrow=5) class1 <- c(rep(0,4),rep(1,4)) col1 <- ifelse(class1 == 0,"blue","red") class2 <- c(rep(1,3),rep(2,5)) col2 <- ifelse(class2 == 0,"yellow","green") heatmap.2(mat,col=greenred(75),ColSideColors=col1,trace="none", dendrogram = "column",labCol = NULL) ----------------------------------- How can I modify the code so that both col1 & col2 are displayed in the heatmap? thanks! [[alternative HTML version deleted]]

Hi, Is there a way I can draw an abline on a heatmap? I try the abline function, but don't get the line. My sample code is: mat <- matrix(sample(1:100,40),nrow=5) heatmap(mat,col=greenred(75),trace="none", dendrogram = "column",labCol = NULL) abline(h=5,v=4) thanks! [[alternative HTML version deleted]]

...ll(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

...e[,-1] > sample.map <- as.matrix(sample.set) ### have to order as i have markers on rows so just want denrogram on triats(column) >ord <- order(rowSums(abs(sample.map)),decreasing=T) >heatmap.2(sample.map[ord,],Rowv=F,dendrogram="column",trace="none",col=greenred(10)) But I want to give colours more specifically as I want to show the QTL hotspots starting as fallow 1) -6 to -4 (blue) 2) -4 to -2 (light blue) 3) -2 to 0 (dark grey or black) 4) 0 to 2 (dark grey or black) 5) 2 to 4 (yellow) 6) 4 to 6 (red)...

...efficients[(clsum[,1]>1) & (clsum[,2]>1) & (clsum[,3]==0),],breaks=c(seq(-2.5,-0.6,0.1), -0.1,0.10,seq(0.6,2.5,0.1)),dendrogram="none",Colv=c(9:12,5:8,1: 4),labRow=rep('',520),margin=c(10,5),colsep=c(4,8),trace="none",density. info="none",col=greenred.colors(40),key=F) > popViewport() viewport[GRID.VP.177] > pushViewport(viewport(layout.pos.col=3)) viewport[GRID.VP.179] > pushViewport(viewport(layout = grid.layout(3, 1, heights = unit(rep(1,3), c("null", "null", "null"))))) viewport[GRID.VP.180] &gt...

Hi, I am using heatmap.2 of gplots to make heatmaps of my the attached file. I am giving my code for the same .. library(gplots) x=read.table("1.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both"), scale = c("row"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(5, 10), xlab = "EXPRESSIONS", ylab = "GENES", labRow = NULL, labCol = NULL, key=T...

...39;green','orange','blue','yellow', 'gray','black','brown','aquamarine3','cyan', 'darkmagenta','darkviolet','green4')) col=colorRampPalette(c("green","white","red"))(256), #col=greenred(75), #col = cm.colors(256), #bgStyle="3D Rectangle", #bgGradientMode=" Diagonal Edge", Rowv=TRUE, Colv=FALSE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale = c("column"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins...

Hi, I am drawing a heat map using gplots of R package. The file (new4) is having values 0 and 1 only. library(gplots) library(marray) x=read.table("new4", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("black","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale = c("row"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(25, 20), #xlab = "" ylab = "" labRow = NULL, labCol = NULL, key=TRUE, keysize=1, d...

...rding to my own requirement as the below code is taking as per the file entries. Any help would be appreciable. library(gplots) x=read.table("final.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("green","white","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale = c("column"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(01, 55), xlab = "", ylab = "", labRow = NULL, labCol = NULL, key=TRUE, keysize...