similar to: About the breakpoint when making heatmap with lots of variables

HI, I am trying to create a heatmap with 24 samples with 15672 varibles, I read in the table in R, and then made it as a matrix, then try to create the heatmap using heatmap(x,...) However, I received the error message as: > heatmap(t(x)) Error: cannot allocate vector of size 936.8 Mb R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error code=12) *** error: can't allocate

Hi All, Please forgive me if this is the wrong group. I did not see a llvm-user group (). The User Guide also lacked a topic (http://llvm.org/docs/userguides.html#userguides). I am an Xcode user. I want to set a breakpoint on malloc_error_break all the time (it makes no sense to re-run after setting the breakpoint on occasion). I want the breakpoint whenever the debugger starts, and for all

On Wed, Nov 14, 2012 at 11:18 PM, Jeffrey Walton <noloader at gmail.com> wrote: > Hi All, > > Please forgive me if this is the wrong group. I did not see a > llvm-user group (). The User Guide also lacked a topic > (http://llvm.org/docs/userguides.html#userguides). > > I am an Xcode user. I want to set a breakpoint on malloc_error_break > all the time (it makes no

I compiled 3.0.6pre1, including the crtimes and fileflags patches for use on Intel OS X 10.5.6, as described by Mr. Bombich (thanks!) here: <http://www.bombich.com/mactips/rsync.html> I want to use 3.0.6 because it seems that this bug: <https://bugzilla.samba.org/show_bug.cgi?id=5365> has been resolved (yay!). ----- [~]$ rsync --version rsync version 3.0.6pre1 protocol version 30

I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: ------------ > dim(as.matrix(data.dcpm)) [1] 15462??? 18 > > heatmap(as.matrix(data.dcpm), col=topo.colors(100)) > heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE,

Hi, I have a question about the heatmap dendrogram in R. I loaded my data matrix in command heatmap(), and it gave me a heatmap accordingly, and the rows (genes) also were clustered accordingly. But now I don't want the genes clustered in that way, I have a new order of these genes, and want the rows of the heatmap are drawed as the order I give. Could anybody help me on that? Thank you!

Hi, I'm kinda new of the R world. I need to use the heatmap or heatmap.2 function to plot correlation values. 2 questions: - how can I specify a color palette? (would like to have a transition from blue(-1) to white(0) to red(1)) - how can I use heatmap.2 imposing a specific order (like hclust.order)? I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to plot them

Hi Sorry to revisit an old problem, I seemed to solve this in 2004, only for it to resurface :-S I am trying 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

Hi, I have what would seem to be a very simple problem but have been unable to find any way to go about solving it: I am using heatmap.2 to create a heatmap and by default the x axis label is at the bottom of the heatmap, I simply want to move the label to the top of the heatmap. Any help with this would be greatly appreciated. Thanks, Mark

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hi, I was trying to use par(mfrow) to put 4 heatmaps on a single page. However, I get one plot per page and not one page with 4 plots. What should I modify? Test code is given below: test = matrix(rnorm(60), 20, 3) pdf(file='test.pdf',width=10,height=8) par(mfrow=c(2,2)) heatmap(test) heatmap(test) heatmap(test) heatmap(test) dev.off() thanks! [[alternative HTML version deleted]]

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 want to generate a heatmap for my data (in a matrix). However, the data has some missing values (represented as blank). I get the following errors (with the blanks and with blanks replaced by NA and including the option rm.na = TURE): > filename = "input_heatmap.txt" > g <- as.matrix(filedata) > fg <- rainbow(nrow(g), start=0, end=.3) > gg <-

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 I am having some problems getting my heatmap to be the right size! Let me explain. I am experienced at getting an hclust or a dendrogram object to be the right size. For example, I have a dataset which has 4000 rows, which I clustered using hclust and I wanted to plot it as a horizontal dendrogram. So I used jpeg(), set the image height to be 4000 and plotted the dendrogram and got the

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

Howdy, I am trying to make a simple monochrome heatmap from 1 row of data. Essentially, I just want a long bar where black represents the max value in the data, white is the minimum, and all values in between are interpolated appropriately. I have tried using heatmap and heatmap.2, but both have issues. heatmap seems to be restricted to only drawing a square plot, and this data requires a

Using the heatmap.2 function, I am trying to generate a heatmap of a 2 column x 500 row matrix of numeric values. I would 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

I'm having trouble with the heatmap function in R. When I try and heatmap something, my graphics window does not open. Does anyone know if this is a glitch in the version of R that I'm using? I've listed my version of R below, as well as a simple heatmap command. I'm running the program on a Mac, OS 10 v 10.3.9. Any suggestions?? Thanks! Peter > version _

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