search for: rowv

...to plot a heatmap, 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]]

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_ dendrogra...

...the distfun and hclustfun 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?...

...trix 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

...d maintainer, 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 r...

...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), na.rm=T) z$Rowv, z$Colv are now dendrograms of the rows and the columns repectively (this couldn't be done with heatmap.2 since it doesn't return the dendrogram objects). and I've tried to create the wanted image using: heatmap.2(Matrix2, symm=T, breaks=20, col=rich.colors(19), main="Matrix2&quot...

...he left-right arrangement of one pair of subclusters (columns) was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite nonexpert, it seems to me that hclust is also invoked by heatmap. > heatmap function (x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL, distfun = dist, hclustfun = hclust, add.expr, symm = FALSE, ... hcr <- hclustfun(distfun(x)) ddr <- as.dendrogram(hcr) .... hcc <- hclustfun(distfun(if (symm) x else t(x))) ddc...

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.t...

...uot;F","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 >...

...krc> # get the correlation matrix krc> m <- cor(dd) a 10 x 10 matrix ; i.e. 10 row units and 10 column units. Hence the following never works, at least not for the heatmap() function as in ``standard R''. krc> # this version works correctly krc> heatmap(m, Rowv=as.dendrogram(hc), symm=TRUE, revC=FALSE, RowSideColors=cols) gives immediately the obvious error Error in heatmap(m, Rowv = ............ : row dendrogram ordering gave index of wrong length krc> #this version reverses the dendrogram and image, but not the colors krc> heatmap(m,...

...lr3 <- 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 sta...

...he 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 <- heatmap.2(x, col=co...

Under Details, the documentation says "[if Rowv or Colv] is 'NULL', _no reordering_ will be done for the corresponding side." In fact, as explained elsewhere in the documentation, 'NA' is required, not 'NULL'. An anonymous expert suggested that I should attach an svn diff file to this report, so I will. JD -------...

...ntal and vertical line that I would like to get rid off. Any suggestions? #my code below my.matrix <- cbind(func.1 = c(1,2,2,1,1,3,1,2,3,1,1,2,2,3,1), func.2 = c(2,2,1,1,3,3,1,1,2,2,1,3,3,2,1)) mycol <- colorpanel(n=3,"green","grey","red") heatmap.2(my.matrix,Rowv=FALSE, Colv="Rowv", col=mycol, trace="both", tracecol="black", key=FALSE, symm=FALSE, vline=NULL, hline=NULL) Kind regards, Peter

...e been trying 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="non...

...map. Each point is either a floating point number or NA. I load the data in with:   data <- read.csv("matrix.csv", sep=',') Convert the data to a matrix with:   data_matrix <- data.matrix(data)  and then produce the heatmap with:   data_heatmap <- heatmap(data_matrix,Rowv=NA,Colv='Rowv',margin=c(0,0)) The heatmap is displayed in a separate window as expected and looks correct apart  from fine white banding lines spaced out evenly over the image running horizontally  across the image? At first I thought it was my data but I checked that and its not. If I re...

> 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 i...

Dear list, I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix x clustered only by columns and keep the original order of rows unchanged. Is there a way to do that in heatmap.2()? Thanks a lot! Any suggestions will be appreciated! Best, Allen [[alternative HTML version deleted]]

Hi, I wanted to draw a heatmap with some horizontal lines. For example: #------ code ------ mat <- matrix(-1:1,7,9) heatmap.2(mat,Rowv=NA,trace = 'none',key=F) #----end code ----- In this heatmap, I want to subgroup the rows. For instance, I would like to group rows 5,6 & 7 together, and would draw a black line between rows 4 & 5 to demarcate the group. Similarly, I want to group rows 3 & 4 in one group, and...

Thanks Tom. heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen, breaks=seq(-1,1,by=0.01), symm=TRUE, trace="none", dendrogram="none") that did the trick :) Begin forwarded message: From: "Leja, Thomas" Date: 29 March 2011 03:47:59 GMT+01:00 To: "Benton, Paul" Subject: Re: [R] comparing heat...