similar to: Modificando heatmaps

Hi I am trying to understand what happen with the heatmap.2 code that it used to work (last used in October 2015). I am able to get a heatmap but my colour key doesn't come up and instead I get an error in all my files the used to work. Does anyone has any idea of what could have changed? or how to fix this. Thanks. # Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :

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'm trying to save heatmaps as PDFs. However, the PDF version of the heatmaps (Heatmap_CAFvsTNF_run2.pdf) is blurred when compared to its counterpart, which was saved manually by using the software "Grab" (Heatmap_CAFvsTNF_run2.tiff). -----R code-------- sample_output <- "stroma_run2" filename <-

Hello, I have a large (919 X 919), hierarchically clustered heatmap that I would like to read the labels off of. I have tried saving the figure in pdf format and enlarging it until I can see the labels, but if I make the labels small enough to read (so that they don't overlap) using cexRow and cexCol, they do not appear in the pdf. The limit seems to be anything below cexRow or Col = 0.06.

Full_Name: Peter Fischer Hallin Version: Version 1.8.1 OS: Irix64 Submission from: (NULL) (130.225.67.236) I've made a script look like this: exp <- read.table("graph/1933672048.cluster.data") exp <- as.matrix(exp) postscript("graph/1933672048.cluster.data.ps") heatmap(exp,scale="none",cexCol=0.4,cexRow=0.2,col=custom,margins=c(5,5)) The row labels

I generated a heatmap in R using the following commands: > mydata <- read.csv(file="Data.csv", header=TRUE, sep=",") > mydata <- mydata[rowSums(mydata[,-1]^2) >0, ] > rownames(mydata)=mydata$Name > mydata <- mydata[,2:253] > mydatamatrix <- data.matrix(mydata) > mydatascale <- t(scale(t(mydatamatrix))) > hr <-

I generated a heatmap in R using the following commands: > mydata <- read.csv(file="Data.csv", header=TRUE, sep=",") > mydata <- mydata[rowSums(mydata[,-1]^2) >0, ] > rownames(mydata)=mydata$Name > mydata <- mydata[,2:253] > mydatamatrix <- data.matrix(mydata) > mydatascale <- t(scale(t(mydatamatrix))) > hr <-

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how

Hello! I looked for help through google and the help-files and spend several hours with trial and error, but didn't find a correct way. It's all about lines in a heatmap to separate different data block from each other to underline the significance of the found clusters! The heatmap is build like that: heatmap(X, Rowv=NA, Colv=NA, symm=TRUE, cexRow=0.3, cexCol=0.3) I switched the

I am using heatmap with the arguments below. The title size stays the same no matter what I set cex.main to. Is this expected? Can I adjust the title size in heatmap? Also, the position of the main title is at the very upper edge of the output and if I use a "\n" to stack the title the upper line is out of bounds and doesn't show up. I am outputting to pdf. Any help? Thanks,

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

hello my name is reynaldo my question is the next. i want change the text of the validations error messages generated by ruby when you don''t wrote properly the data in the form. -- Posted via http://www.ruby-forum.com/.

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

Hello R-Community, I am a rookie in R and I am fascinated with the power of bio computing by R. I am analysing gene expression data from Real time PCR. I have used absolute gene quantitation to measure gene copy number in all my transcripts. All my data has been normalised them to a housekeeping gene, which is constitutive expressed. My problem is as follows. After normalising some of the genes

Hello, I have a large data set from RNA sequencing and I am trying to make a heat map of my data. I have am having issues formatting my heat map figure. My data set is large with the log2 fold change for over 6oo genes across 4 treatments. My csv file is formatted as such: Gene Drought Ozone Temp1 Temp2 Glyma0041s00260

Hola a todos, Quisiera juntar las informacion de dos data.frames con una union de columnas un tanto especial. La informacion que tengo son datos de captura-recaptura de diferentes individuos, por ejemplo en una base de datos tengo:ID <- c(1,2,3,4)Fate_1 <- c(2,2,2,2)Fate_2 <- c(0,0,0,NA)Fate_3 <- c(0, NA, NA, NA) y en otra base de datos tengo:ID <- c(1,2,3)Fate_1 <- c(0, 0, 0,

Hola He hecho el típico mapa con gadm y spplot: library(sp) ES <- local(get(load(url("http://biogeo.ucdavis.edu/data/gadm2/R/ESP_adm2.RData ")))) acerco las canarias: A <- which(ES en data$NAME_1 == "Islas Canarias") L <- length(ES en polygons[[A]]@Polygons) L <- length(ES en polygons[[A]]@Polygons) for (i in 1:L){ ES en polygons[[A]]@Polygons[[i]]@coords

Hi, I would like to change the font type (to courier) of my rows labels when I plot a heatmap with R. I have used cexRow=0.7 to modify the size but didn't find anything regarding font type. heatmap(as.matrix(cebpa50), margins=c(5,10) , Colv=NA , scale="column", col=col4, cexRow=0.7) Thanks, Ben

Hola, Perdonar por saltarme algun paso, pero a veces no me doy cuenta que yo lo tengo muy claro porque soy el que tiene el problemay no termino de explicarlo del todo jeje. Ahora he adjuntado los pasos necesarios en excel para obtener el resultado que quiero , serian 5 pasos: Quizas en R haya otra manera mas rapida. 1) Cargar las dos bases de datos (base de datos ver y base de datos azul)2) Hacer

Hello Gurus I have two correlation matrices 'xa' and 'xb' set.seed(100) d=cbind(x=rnorm(20)+1, x1=rnorm(20)+1, x2=rnorm(20)+1) d1=cbind(x=rnorm(20)+2, x1=rnorm(20)+2, x2=rnorm(20)+2) xa=cor(d,use='complete') xb=cor(d1,use='complete') I want to combine these two to get a third matrix which should have half values from 'xa' and half