search for: colsidecolor

Hello again, lately I have been playing a lot with heatmap functions, in particular I complemented heatmap.2 with a nice feature from heatmap.plus, i.e. the possibility of assigning a matrix to ColSideColors so to take into account more annotations. Below is the code I introduced in heatmap.2, everything else is maintained equal to heatmap.2: if (!missing(ColSideColors)) { #if (!is.matrix(ColSideColors)) #stop("'ColSideColors' must be a matrix") if (!i...

...-------- 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]]

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem: cU <- cor(USJudgeRatings) sideCols <- rainbow(ncol(cU)) heatmap(cU, symm = TRUE, distfun = function(c) as.dist(1 - c), ColSideColors=side...

I am in a situation needing 3 ColSideColors for heatmap.2. How can I do that? TIA Daren

...n I tried to plot two different color bars, the one corresponding to "cm.colors(10)" is not correct (it starts with one black and one red.? Not sure where they're from?) Any ideas? Thanks! ...Tao library(heatmap.plus) set.seed(1234) x <- matrix(rnorm(400), ncol=10) heatmap(x, ColSideColors= cm.colors(10), Colv=NA) heatmap.plus(x, ColSideColors=cbind(cm.colors(10), cm.colors(10)), Colv=NA) heatmap.plus(x, ColSideColors=cbind(rep(1:2,each=5), cm.colors(10)), Colv=NA)

...in heatmap? Also, the position of the main title is at the very upper edge of the output and if I use a "\n" to stack the title the upper line is out of 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-gn...

...a = TURE): > filename = "input_heatmap.txt" > g <- as.matrix(filedata) > fg <- rainbow(nrow(g), start=0, end=.3) > gg <- rainbow(ncol(g), start=0, end=.3) > hg <- heatmap(g, col = cm.colors(256), scale="column",na.rm = TRUE, + RowSideColors = fg, ColSideColors = gg, margin=c(5,10), + xlab = "Average per Species", ylab= "Pathways", + main = "heatmap(<Ka/Ks Average Data per Species>, ..., scale = \"column\")") Error in heatmap(g, col = cm.colors(256), scale = "column", na.rm = TRUE, : '...

Can someone recommend a more sophisticated way to annotate heatmaps than the ColSideColors argument of heatmap and heatmap.2? In particular, I would like to be able to annotate columns with more than one piece of information, like in Figure 1 of the article at http://www3.interscience.wiley.com/cgi-bin/fulltext/117905619/HTMLSTART / doi:10.1002/hep.22256. Some example data and a heatm...

...left corner. Notice I have added side bars to the heatmap, but how could I move the color key below the image? ------ library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x), start=0, end=.3) res=heatmap.2(x, RowSideColors=rc, ColSideColors=cc)   Thank you very much,   Pingping Qu ----- Cancer Research And Biostatistics (CRAB) Seattle, WA 98101  ------- [[alternative HTML version deleted]]

I am using attributes colsep and sepwidth from heatmap.2 function, however when using larger values for sepwidth the following columns are not moved to the right but the seperator is covering the column(s) with a white bar and the column labels and ColSideColors remain at their positions, is this intended? I expected the following columns to be shifted to the right by sepwidth. Is there a way to achieve this? Here is a simple example library(gplots) col <- c( rgb(0,100:0,0,maxColorValue=100), rgb(0:100,0,0,maxColorValue=100) ) heatmap.2(matrix(c...

...ve been using: tmp <-read.table("Heat.txt",row.names=1,header=T) mydata <- data.matrix(tmp) rc <- rainbow(nrow(mydata),start=0, end=1) cc <- rainbow(ncol(mydata), start=0, end=1) hv <- heatmap(mydata, col = cm.colors(256), scale="column", RowSideColors = rc, ColSideColors = cc, margin=c(5,10), xlab = "Gene", ylab= "Species", main = "Heatmap", reorderfun = function(mydata,w) reorder(mydata,0.0:100.0), Colv=NULL, Rowv=T) Thnak you, Fearon Cassidy Department of Zoology Trinity College Dublin [[alternative HTML version deleted]...

...matrix, 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 to do this in R? Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are difficult to read. I used cexRow = 0.01 and...

....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 to do this in R? Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are difficult to read. I used cexRow = 0.01 and...

.... here is a reproducible example from the help page library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x), start=0, end=.3) hv <- heatmap.2(x, col=cm.colors(255), scale="column", RowSideColors=rc, ColSideColors=cc, margin=c(5, 10), xlab="specification variables", ylab= "Car Models", main="heatmap(, ..., scale=\"column\")", tracecol="green", density="density") This gives me a heatmap similar to the 9th...

...quot;none", xlab="individuals", ylab="genes", main="heatmap", density.info="histogram", col=redblue) dev.off() ------------------------------------------------------------------------------ I have two problems now: 1) I don't know how to use the 'ColSideColors' option to emphasize the 'groups' rather than 'each individuals'. 2) When I only included 100 genes in my heatmap, I had no problems getting the 'color-key'; However, when I included more genes (i.e., 300 genes), I can NOT get the 'color-key' any more, even that...

...ing, but I prefer to continue with what we have been using). Anyway, if anyone knows a package that will read in cluster files in a format that I can use to create a heatmap using the "heatmap" method, I would greatly appreciate the info. Or, if anyone know a way to add the equivalent of ColSideColors from "heatmap" in Java TreeView, that would be equally helpful. Thanks! Mark

....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] "di" "distfun" "hcc" "hclustfun" [21] "...

...ap.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 these two command lines, hr <- hclust(as.dist(1-cor(t(mydatascale), method="pearson")), method="complete") hc <- hclust(a...

Hello! I looked for help through google and the help-files 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

I have a data set with 6 variables and 251 cases. The people who supplied me with this data set believe that it falls naturally into three groups, and have given me a rule for determining group number from these 6 variables. If I do scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...)) stuff.dist <- dist(scaled.stuff) stuff.hc <- hclust(stuff.dist)