similar to: heatmap and hclust

Good afternoon, I ran heatmap and hclust on the same matrix x (strictly, I ran heatmap(x), and hclust(dist(t(x))), and realized that the two dendrograms were slightly different, in that the 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

Hi netters, I have a matrix X of the size (1000,100). The values are from -3 to +3. When I tried heatmap(X, distfun=function(c),dist(c,method="bin"),hclustfun=function(m),hclust(m,method="average")) I got the error message: Error: evaluation nested too deeply: infinite recursion / options(expressions=)? However, if I used default parameters for distfunction:

Hi, Could you please help? Heatmap doesn't work with: > heatmap(as.matrix(SPIV2),na.rm = T) Error in hclustfun(distfun(x)) : NA/NaN/Inf in foreign function call (arg 11) There are no 0 data rows or column Thanks a lot Regards --------------------------------------- David

Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried >heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in

Hi, I run into following error when using heatmap() for data matrix "xx". Any help is appreciated? "xx" contains many "NA"s. > hv <- heatmap(data.matrix(xx)) Error in hclustfun(distfun(if (symm) x else t(x))) : NA/NaN/Inf in foreign function call (arg 11) Thanks a lot. Yuhong

Hello does anyone know what algorithm is used to produce the hierarchical clustering in the gplots package using the function heatmap.2? I think it may be the complete linkage clustering algorithm, but I can't find a source that seems reliable. Thank you and sorry if I posted this in the wrong place. If I have, please let me know and I will move it to the appropriate list. -- View this

Hi, I am using the function heatmap(stats) to draw a microarray heatmap, columns are samples and rows are gene features. I did a 2D clustering during the heatmap drawing. The features and samples indeed cluster into several blocks both vertically and horizontally. I can get the index of re-ordered rows and columns after the heatmap drawing by typing the the return variable of the heatmap

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",

Dear all, the default plotting method for hclust trees looks just fine for few objects like in the example dataset. But when it comes to many objects (some 1000 - I'm trying to visualize clustered microarray data) it renders a tree, that one cannot inspect, because of overlapping text and lines. My question is, is there a way or a plotting parameter for plotting a tree which is wide enough

Hi, Can someone please guide me towards how to produce "heatmap" output from the output of "hclust" run prior to the actual "heatmap" call? I have some rather lengthy clustering going on and tweeking the visual output with "heatmap" recalculating the clustering every time is not feasible. Thanks, Joh

Hi, I am having troubles with heatmap(). I have a matrix containing pairwise distance values and I want to plot this matrix with heatmap. I wonder now what distfun is for. Is a distance matrix computed from my initial matrix again and then plotted? cheers, andreas

I have written a wrapper for heatmap.2 called heatmap.w.row.and.col.clust which auto-generates breaks using breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, digits = 2) #(stddev in this case = 2.5) This has always worked well in the past but now I am getting an error that non-finite breaks are being generated. Drilling down, it seems that my wrapper is generating finite

Hi all, By default, the heatmap function gives an image with a dendrogram added to the left side and to the top. Is it possible to only add the dendrogram to the left side and let the order of the columns unchanged ? I tried heatmap(mat, col=rbg,Rowv=res.hclust$order,Colv=1:dim(mat)[[2]]). In this case, the order of the columns are unchanged but a dendrogram is added to the top. How can I

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 <-

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,

Hi there, I am interested if there is anyway to keep track of the occurrence of warning message. I know that warnings will only be printed out at the end of the program if warn=0. However I am also interested at which particular set of data does the warnings occur too. This is because I am running 1000 data, so if there are 2 or 3 data that give warnings, I would like to know which are the ones

Hi All Not sure if this a bioconductor question or general R mailing list so apologies if this has gone to the wrong one................. When plotting dendrograms created by hclust you can "identify" clusters by clicking on the graphics and returning a list of what is contained in each cluster. However I'd like to be able to "zoom in" on specific clusters and plot

Could any one tell me there is a search function for R-help Archives? Thanks

I am trying to build hdf5 for ms-windows. I downloaded the hdf5_1.4.7.tar.gz, gunzipped it and got a tar file. I extracted everything into a directory tree called hdf5. I also found a Makevars.win and libhdf5.def in the R help archives from March 2002. I put those two in hdf5 as well. I issued the command Rcmd build --binary hdf5 but got this message complaining it can''t find

Hi, I get an error saying " Cannot allocate vector of size 71289kb". So I tried to increase memory by memory.limit(size=3000000000), I also tried other numbers. Each time I get the message NULL and then I still get the same error as above. I'm using Windows 2000. The system has 1G RAM, and 1.6GHz processor. I was only running R, and was trying to do use a BioConductor package. I