similar to: Z score in gplots

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",

Hi, I am drawing a heat map using gplots of R package. The file (new4) is having values 0 and 1 only. library(gplots) library(marray) x=read.table("new4", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("black","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale =

Dear Experts, I am using the below script to generate the heat map of gene expression data. I am using Hierarchical Clustering (hclust) for clustering. Now I want to compare different clustering parameters such as *K-means* clustering, Model Based Clustering, I have two queries: 1. How to incorporate different clustering method in the same code? 2. Is this possible to implement pvclust in the

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

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 wanted to make more than one side color bar. For example, I can make one side color bar (col1) with the following code: ----------------------------------- library(gplots) mat <- matrix(sample(1:100,40),nrow=5) class1 <- c(rep(0,4),rep(1,4)) col1 <- ifelse(class1 == 0,"blue","red") class2 <- c(rep(1,3),rep(2,5)) col2 <- ifelse(class2 ==

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.

Hi, Is there a way I can draw an abline on a heatmap? I try the abline function, but don't get the line. My sample code is: mat <- matrix(sample(1:100,40),nrow=5) heatmap(mat,col=greenred(75),trace="none", dendrogram = "column",labCol = NULL) abline(h=5,v=4) thanks! [[alternative HTML version deleted]]

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) %||%

I am using attributes colsep and sepwidth from heatmap.2 function, however when using larger values for sepwidth the following columns are not moved to the right but the seperator is covering the column(s) with a white bar and the column labels and ColSideColors remain at their positions, is this intended? I expected the following columns to be shifted to the right by sepwidth. Is there a way

Dear all, I have installed R using yum install R-2.9. I am able to use R for general functions but when I installed some library say gplots I am getting the below error. > install.packages("gplots") Warning in install.packages("gplots") : argument 'lib' is missing: using '/home/fedora/R/i386-redhat-linux-gnu-library/2.11' Warning: unable to access index

I'm suppressing the labeling of my rows and columns in heatmap.2 using the commands: labRow = " ", labCol = " " But I'd like to annotate them again using the axis command: axis(1, at=seq(500, 1000, 500)) mtext("Group 1", "Group 2") For some reason however it appears that the axis command is having no effect. My complete

Dear all, I have a set of five datasets with string, for which I need to draw the venn diagram. there are tools available to draw venn diagram online, but limited to three sets. I can also generate venn for three from limma package, but do not know how to proceed with five subsets. Help me in drawing the same any script . Thank you Khush [[alternative HTML version deleted]]

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

On the cover of Zivot and Wang's Modeling Financial Time Series with S Plus, there is a correlation plot that seems to indicate the strength of correlation with color-coded squares, so that more highly correlated stocks appear darker red. If anybody out there is familiar with the book or understands what I am talking about, I am curious as to whether or not there is a similar function in R

Hi folks, I am wondering if the following is possible: I want to control the arguments sent to a function by string variables. For example, instead of > heatmap.2( A, col=greenred(75) ) I would want to have something like: > heatmap.2 ( paste(A, "col=greenred(75)", sep=",") ) Is this possible to do that? Thanks, D.

Hi, I''m using heatmap.2 to cluster my data, using the centroid method for clustering and the maximum method for calculating the distance matrix: library("gplots") library("RColorBrewer") test <- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77, 0.08, 0.96, 0.51, 0.51, 0.14, 0.19, 0.41, 0.51), ncol=4, byrow=TRUE)

I would like to use gridBase to place four separate heatmaps (actually, a stripped-down heatmap.2 from ght gregmisc package that contains only the "image" part) into four different viewports. I can get the placement correct, but I keep 'losing' the previous plot. Any suggestions? Here is some quick example code trying to put a heatmap into the left viewport and then

Hi, i created a graph with heatmap(sma) function: heatmap(dataHeat(x)) and I wish to change the gradation of colors from blue to red, how could i do? Using "heatmap(dataHeat(x), col=c(2,4))" i will use only 2 colors without gradation. Ty so much Andrea

Dear All: I tried to use heatmap.2 to generate hierarchical clustering using the following command: heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) datamatrix is subset of a RMA normalized data subset by a genelist. The problem is a lot of times, the z-score in key are from, like -5 to 15 or