similar to: gplot 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",

Hi, Can anyone tell me how to set Z-score according to my own requirement as the below code is taking as per the file entries. Any help would be appreciable. library(gplots) x=read.table("final.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("green","white","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist,

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

Hi all , I have following script to plot some data. plot( c(1,1100), c(0,15), type='n', xlab='', ylab='', ylim=c(0.1,25) , las=2) axis (1, at = seq(0,1100,50), las =2) axis (2, at = seq(0,25,1), las =2) lines( c(1,304),c(0,0),col='grey', lwd=3 ) lines( c(1,238),c(1,1),col='grey', lwd=3 ) segments(86, 0 ,270,col = "green", pch=23,

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]]

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 ==

Hi, I am using vim to edit my files...I do not know what has been pressed by me as my R code get converted to such a crap... %PDF-1.4 %<81>â<81>ã<81>Ï<81>Ó\r 1 0 obj << /CreationDate (D:20100902122215) /ModDate (D:20100902122215) /Title (R Graphics Output) /Producer (R 2.11.1) /Creator (R) how to reconvert it to the my actual code?? as I do not have backup for

Hi Folks, I'm contemplating using locator() to digitise external graphics. To set context, I would be using X11 display on Linux. To pre-empt the obvious comment: I've found on the R site the suggestion to use the 'pixmap' package. I've tried this, and it works; but it involves building a big R object (the internal pixmap representation), and this chokes my somewhat puny

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

Can any one help it will be very kind, loop statements I have this table and some more records, I want to reshape it V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 TP53 Dis1 Dis2 Dis3 Dis4 Dis5 Dis6 DCI New1 New2 New3 New4 FDI Hi2 H3 H4 GHD I1 I3 I4 I5 I6 I7 I8 I want my new table or matrix to be some thing like this V1 V2 V3 Tp53 Dis1 Dis2 Tp53 Dis1 Dis3 Tp53 Dis1 Dis4 Tp53 Dis1 Dis5 Tp53 Dis1 Dis6 Tp53 Dis2

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.

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) %||%

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

I have a couple of devices that need an analog modem to communicate outside of our Asterisk system. Most FXS gateways don't seem to support this... I have a stack of Sipura 2002's that are, AFAIK, worthless for this purpose. I've heard that Digium's IAXy FXS will work with modems, but I can't find any reference to that in their documentation. There is also the

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.

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

Dear all, I'm generally not a big fan of GUIs, but I have just discovered one thing where a GUI would be a nice thing: creating color palettes. I'm creating an "image", for transparencies for a lecture I'm giving, so this is going to look great... :-) What I'm out for, is to make green tones and red tones, and a relatively sharp break between them. This break will

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

Hi all, I am a bit mystified by this error message that I get when I try to apply lmer() to a simple dataset with one between factor (age) and one within factor (item): "$ operator is invalid for atomic vectors" I'll just provide the code, because I don't see where the problem is: library(lme4) options(contrasts=c("contr.helmert","contr.poly")) data =