similar to: image function help required

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

Hi, I'm stuck with parsing data into R for heatmap representation. The data looks like: 1 id1 x1 x2 x3 .... x20 2 id1 x1 x2 x3 .... x20 3 id1 x1 x2 x3 .... x20 4 id1 x1 x2 x3 .... x20 ......... 348 id2 x1 x2 x3 .... x20 349 id2 x1 x2 x3 .... x20 350 id2 x1 x2 x3 .... x20 351 id2 x1 x2 x3 .... x20 ......... The data is sorted for the IDs (id1,id2 .....id40) and I like to

Dear R users, I am trying to print heatmaps in a loop (with a pause). Idea is to visualize changing correlations over time and for testing I wrote this simple (reproducible) code below. My problem is that levelplot() does not produce any output when I run the code (though heatmap does). Ideally I would like to use levelplot() as it produces a neat index on the side indicating the color and the

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 !=

Hola a todos, Estoy trabajando con la función heatmap.2() de la libreria ggplots. A continuación encontrarán un ejemplo de la estructura de mis datos y el código para generar el gráfico que me gustaría modificar: # Datos set.seed(123) x <- matrix(rnorm(8*30), ncol = 8) rownames(x) <- paste(''GM10A'',1:30,sep="") colnames(x) <-

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

Hello, please see below my code for a heatmap. Unfortunately my column names do not completely appear. Can you please send me the appropriate code to visualise them? Many Thanks! Nils library(GMD) dat<-data.frame(EntryA=as.numeric(c(4.24,3,1.66,1.28,1.2,-1.32,-1.88)), EntryB=as.numeric(c(4.16,4.82,-1.82,-3.02,0.99,1.1,-3.31)))

Hi! I'm displaying a contingency table with heatmap(): > svm.predPix.tabla svm.predPix CC DD LL NN NN2 CC 22 0 3 8 3 DD 0 27 0 1 0 LL 1 1 90 3 7 NN 2 0 1 11 4 NN2 0 0 5 1 20 > heatmap(svm.predPix.tabla[5:1,], Rowv=NA, Colv=NA,col = rev(heat.colors(32)), scale="column", margins=c(5,10)) and I'm happy

Hi all, I am interested in plotting a heatmap of a set of genes. I would like the text labels of these genes to be colored red rather than black if they meet certain statistical criteria (using an if statement). I'm not sure how to change individual color labels without changing them all. Can anyone provide some insight on how to do this? Thanks in advance, Jake

Dear All, There might be a bug in heatmap(): x <- matrix(rnorm(10*5), 10, 5) heatmap(x, labCol=1:5) Error in axis(1, 1L:nc, labels = labCol, las = 2, line = -0.5, tick = 0, : 'at' and 'labels' lengths differ, 5 != 10 Works fine under 4.0.1. Looking at the code from 4.0.1 vs. Rdevel, esp. this part sticks out: labRow <- labRow[rowInd] %||% rownames(x) %||%

Hello again, lately I have been playing a lot with heatmap functions, in particular I complemented heatmap.2 with a nice feature from heatmap.plus, i.e. the possibility of assigning a matrix to ColSideColors so to take into account more annotations. Below is the code I introduced in heatmap.2, everything else is maintained equal to heatmap.2: if (!missing(ColSideColors)) { #if

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

Hi all, I'm trying to figure out a way to create a data graphic that I haven't ever seen an example of before, but hopefully there's an R package out there for it. The idea is to essentially create a heatmap, but to allow each column and/or row to be a different width, rather than having uniform column and row height. This is sort of like a Marimekko chart in appearance, except that

hi, I have a positive integer matrix like: test<-matrix(c(1,2,2,2,2,1,1,2,3),3) and based on the distant function I made like this: generateDistMat<-function (target) { n <- nrow(target) rn <- rownames(target) distM <- matrix(NA, n, n) diag(distM) <- 0 for (i in 1:(n - 1)) for (j in (i + 1):n) { distM[i, j] <- length(which(target[i, ] !=

Hello, I have encountered some unexpected behaviour with levelplot that may simply be a misunderstanding on my part. If I create a levelplot from a matrix with named columns, some "padding" space appears at the top and bottom of the heatmap. Here is an example, and I've used panel.fill to make the space I'm speaking of evident (in green).

Hi, How do I anchor z=0 to the white color in a levelplot so that the color changes from cyan to magenta precisely as z changes from negative to positive? Also is it easy to change color scheme, say to blue/red as it's more dramatic? Is there a better function for showing heatmap with a color bar? Thanks in advance for any help, I've played with image, heatmap and levelplot a little and

Dear R users, I have a question regarding how to make row labels readable in a heat map. I have successfully made a heat map using function "heatmap.2" in the package "gplots". However, as there are many rows in the heat map, I have difficulties labeling them (heatmap.2 provides a parameter "labRow" to label the row names, but as I have too many rows, I can not make

Hi there, as I'm not sure to understand the coloring levelplot uses, I'm looking for another easy way to create a heatmap like this: library(lattice) mat <- matrix(seq(1,5, length.out = 12), nrow = 3) mat[1,2] <- 3.5 my.at <- seq(0.5,5.5, length.out = 6) my.col.regions <- rainbow(5) graph <- levelplot(t(mat[nrow(mat):1, ] ), at = my.at, col.regions = my.col.regions)

Dear R Community, I am trying to create an heatmap for the following set of data: ##example of data matrix o4 V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 green 27 28 29 29 28 28 26 25 25 23 23 22 22 21 21 22 22 22 yellow 6 8 8 7 7 7 6 6 6 7 7 7 6 6 6 6 6 5 red 15 15 15 15 15 15 14 13 12 11 12 10 9 8 7 6 8 9 pink

The function heatmap() allows to specify row/column labels via the options labRow/labCol. From the code of heatmap(), I understand that when no labels are specified, the row/column labels (or indices) of the input matrix are taken as labels and re-ordered together with the rows and columns of the matrix before plotting, whereas labels supplied via labRow/labCol are plotted in the original order.