search for: colv

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 reorde...

...eatmap, and I don't want the columns of my matrix re-ordered. The function doesn't seem to behave as the help would have you believe: a <- matrix(rnorm(100),nr=20) a.d <- dist(a) a.hc <- hclust(a.d) a.de <- as.dendrogram(a.hc) # columns are re-ordered heatmap.2(a, Rowv=a.de, Colv=FALSE) # columns are re-ordered heatmap.2(a, Rowv=a.de, Colv=1:5) # columns are re-ordered heatmap.2(a, Rowv=a.de, dendrogram="row") # error heatmap.2(a, Rowv=a.de, Colv=FALSE, dendrogram="row") Thanks in advance Mick [[alternative HTML version deleted]]

...e bar heights are a given pig's "gain", "type" identifies groups, and the color depends on "day". i would expect to get the five bars colored red, green, red, followed by two whites. instead, i see: red red white red white. (i am aware that in the code below "colv", the color vector, contains NAs, but that does not seem to be the source of the problem). i would be grateful for any help. alejandro # pigs.dat pig type day gain 1 1 1 1 2 1 1 6 10 1 3 7 a B NA 3 b B NA 4 pigs <- read.table("~/pigs.dat", h=T...

...ner, I was unsuccessful in finding any contact information. The preliminary documentation for heatmap.2 is inconsistent in at least a couple of places when discussing the suppression of one or more dendrograms (and column/row ordering in general). In the Details section, in regards to the Rowv and Colv parameters, "If either is NULL, no reordering will be done for the corresponding side." The default value for these parameters is NULL. With NULL, the dendrograms are computed (and hence reordering is done). In the Arguments section, Rowv shows "determines if and how the row dendro...

Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram="row",col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original order without any dendrogram. For the above statement i am getting an error: Error in image.defau...

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100, pointsize=9) library(gplots) library(RColorBrewer) data <- read.table(inputfile...

...un with the default settings. Is that the same as doing the below? > hr<-hclust(as.dist(1-cor(t(data), method="pearson")), method="complete) > hc<-hclust(as.dist(1-cor(data, method="pearson")), method="complete) > heatmap.2(data, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), scale="row") When I just do the following, I get a completely different heatmap: > heatmap.2(data, scale="row") Could you please tell me how calling the heatmap.2 without specifying the Rowv and Colv results in different heatmaps? The help page says that...

...s For the first matrix I'm using the default clustering and column denrogram options: heatmap.2(Matrix1, symm=T, breaks=20, col=rich.colors(19), main="matrix1", density.info="histogram", denscol="black", trace="none", na.rm=T, dendrogram="col", Colv=T) I would like to show the second matrix with the same row and column ordering of the first matrix. I've tried using the following to create dendrogram objects of the first matrix: z=heatmap(Matrix1, keep.dendro = T, symm=T, breaks=seq(min(Matrix1),max(Matrix1),len=20), col=rich.colors(19),...

...e 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

I want to plot a heatmap without reordering the columns. This works fine in "heatmap": > heatmap(meanX[selected,], col=cm.colors(256), Colv=NA) But in "heatmap.2" I get: > heatmap.2(meanX[selected,], col=cm.colors(256), Colv=NA) Error in if (!is.logical(Colv) || Colv) ddc <- reorder(ddc, Colv) : missing value where TRUE/FALSE needed (Note that instructions for the use of "Colv" and "Rowv" are id...

...t 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)

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 <-

...,"G","I","H","J","K","L","M","N","O","P") par(fin=c(8.0,8.0)) cp <- colorRampPalette(c("white","springgreen","darkgreen"),space="Lab") heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200)) I defined the figure region to make sure that each position is a square. But with these settings I get the following output (though it looks nice): > x <- rnorm(256) > nx <- x + abs(min(x)) > nnx <- 255/max(nx) * nx > x <- mat...

...dendro.leaf('r3') nr1 <- dendro.merge(lr2, lr3, 0.1) nr2 <- dendro.merge(lr1, nr1, 0.3) plot(nr2) x <- matrix(seq(-1, 1, length.out=9), nrow=3) rownames(x) <- paste('r', 1:3, sep='') colnames(x) <- paste('c', 1:3, sep='') heatmap(x, Rowv=nr2, Colv=nc2, scale='none') order.dendrogram(nr2) unlist(nr2) ############### begin output from run of code above ################## > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status...

...ol=1, saturation = 0.85) { if (n < 2) stop("n must be greater than 2") n1 <- n%/%2 n2 <- n - n1 c(hsv(low.col, saturation, seq(1,0,length=n1)), hsv(high.col, saturation, seq(0,1,length=n2))) } # make the heatmap hv <- heatmap(as.matrix(data), Rowv=genes.dendrogr, Colv=samples.dendrogr, col=my.colors());

...I'm not producing the dendrogram as part of the heatmap. What am I missing? ################################### R version 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 &l...

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)

...ying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following: library(gplots) dat<-cor(matrix(rnorm(100, m=10), nrow=10)) mat<-cor(matrix(rnorm(100), nrow=10)) dev.new() heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none", dendrogram="none", main = paste("Correlation Matrix for time delay at ", sep="")) dev.new() heatmap.2(dat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none", dendrogram="none",...

...rt[GRID.VP.177] > pushViewport(viewport(layout.pos.col=1)) viewport[GRID.VP.178] > par(omi=gridOMI(),new=T) > my.heatmap(eb$coefficients[(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(...

> Dear expeRts, > > Currently, my colors are as follows: > mycol <- > c("blue1","blue2","blue3","blue4","black","yellow4","yellow3","yellow2","y > ellow1") > heatmap(snp, Rowv=NA, Colv=NA, col=mycol) > > However, I would like to have the following colors: > bright blue -> dark blue: for intensity range from 0 to 2 in steps of 0.5 > (i.e. 4 grades of blue) > black: for intensity 2 > dark yellow -> bright yellow: for intensity range from 2 to 8 in steps o...