similar to: heatmap with values

Hi, I have searched for a solution but I failed to find an answer. I am hoping you may be able to help me. I have a data set where I have observations for a number of units (n =~40) over a period of time (t =~100) and I have a variable (Z) that codes a categorical variable for each observation. I want to produce a 2D plot where time is on the x-axis and units are on the y-axis. Then each block

Hello! I have data containing a large number of probabilities (about 60) of nonzero coefficients to predict 10 different independent variables (in 10 different BMA models). i've arranged these probabilities in a matrix like so: (IV1) (IV2) (IV3) ... p(b0) p(b0) p(b0) p(b1) p(b1) p(b1) p(b2) p(b2) p(b2) ... where p(b1) for independent variable 1 is p(b1 !=

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 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 reordered.

Hi all, I am a novice user of the heatmap.2 function in the Bioconductor gplots package. I am trying to create a heatmap diagram from a hierarchical clustering result based on the complete linkage and the pearson correlations as the distance metrics. After reading the help page for heatmap.2, it seems that it calls the distfun and hclustfun with the default settings. Is that the same as doing

Hi guys of the R-Help-Team!<br /><br />First of all - you do a great job!<br />I've found a lot of your mails in the internet. So I thought it would be a good idea to ask you a question about R.<br /><br />R is new to me, so sorry, if the question is too simple :)<br /><br />I have a matrix.<br />I can make a 2D Heatmap of this matrix.<br

Dear R users, I'm trying to create images of 2 symmetrical matrices using heatmap.2 of the 'gplots' library. Both matrices have the same row and column names 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",

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,

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

Full_Name: Shane Neph Version: 2.2.1 OS: mac os x Submission from: (NULL) (71.113.43.247) While I found the names of the package authors and 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).

Hello, I have two questions. I'd like to visualize data with a heatmap and I have the following testcase: x <- rnorm(256) nx <- x + abs(min(x)) nnx <- 255/max(nx) * nx x <- matrix(nnx, 16, 16) rownames(x) <-

Hi, I am trying to create a heatmap with some specific requirements. Specifically, I need to be able to center the color-scale around 0, and I need to truncate the data so that a few extreme values do not cause the rest of the heatmap to appear black (on a red/green scale). After reading through and experimenting with heatmap, heatmap.2, heatmap_plus, and heatmap_2, I believe heatmap.2 will

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

Dear all, Objective: I am trying to learn about neural networks. I want to see if i can train an artificial neural network model to discriminate between spam and nonspam emails. Problem: I created my own model (example 1 below) and got an error of about 7.7%. I created the same model using the Rattle package (example 2 below, based on rattles log script) and got a much better error of about

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

> 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 ->

Hello, I've been clustering my data using hclust and cutting the resulting tree with cutree. Separately, I visualize the clusterings with heatmap. Is it possible to have the dendrogram on the heatmap reflect the cutree results? That is, instead of having one large dendrogram, it would have 4 or 25 in the example below. Any guidance on if that's possible or not, and what kinds of

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 -------------- next part -------------- Index:

Hi there, I have a matrix like this: > a4[1:20, 1:5] 194 211 294 314 315 GO:0000003 1 1 1 1 1 GO:0000072 0 0 0 0 0 GO:0000076 1 0 0 0 0 GO:0000082 1 3 1 1 1 GO:0000083 1 0 0 0 1 GO:0000086 0 1 0 1 1 GO:0000114 0 0 0 0 0 GO:0000115 0 0 0 0 0 GO:0000117 0 0 0 0 0 GO:0000160 0 0 1 0 0