search for: labcol

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) %||% (1L:nr...

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 ori...

...run the heatmap code: x <- as.matrix(o4) ramp <- colorRamp(c("yellow","green","blue")) cv<-rgb( ramp(seq(0, 1, length = 83)), max = 255) heatmap(x, col = cv, Colv=NA, Rowv=NA,xaxt="n", yaxt="n", scale="column", margins=c(5,10), labCol=NA,xlab = "Time", ylab= "Colors", main = "") I have quite few problems to change the column names. Being 450 timepoints too many to be readable on the plot, I wanted to reduce/scale them to, let say 45. So, as you can see from the code above, I have removed the...

...2 Lynx 0.50 0.57 0.54 0.59 0.5 0.59 I use the following commands to generate my heatmap: heat <- read.table('temp.txt') x <- as.matrix(heat) heatmap.2(x, keysize=1.2, dendrogram="none", trace="none", Colv = FALSE, main = "Silly Data", labCol= NULL, margin=c(7,8)) This generates a very nice heatmap, but there is one thing I have an issue with: How do I get rid of the 'X' that seems to come automatically before my numeric column values? I just want those columns to be labeled 1905, 1910, 1950, and so on. I cannot find anything i...

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 code is: hv <- heatma...

...p(0,4),rep(1,4)) col1 <- ifelse(class1 == 0,"blue","red") class2 <- c(rep(1,3),rep(2,5)) col2 <- ifelse(class2 == 0,"yellow","green") heatmap.2(mat,col=greenred(75),ColSideColors=col1,trace="none", dendrogram = "column",labCol = NULL) ----------------------------------- How can I modify the code so that both col1 & col2 are displayed in the heatmap? thanks! [[alternative HTML version deleted]]

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]]

...of a function and wanted to see specifically where the maximum posterior probability is. data=read.table("PosteriorData",header=F) mat=as.matrix(data) heatmap.2(mat/max(mat,na.rm=T),dendrogram=c("none"),trace=c("none"), Rowv=F,Colv=F,labRow=3*c(10:-10),labCol=3*c(-10:10),symm=T,col=rainbow(100)) As the values are largely dispersed, I proportioned them to the maximum posterior value (matrix/max value matrix) so that the max value would be 1. I'd like this point to show up as say black on my heatmap. Is there a way I can do this? Set value=1 as bl...

...ot;\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, Mark heatmap(x = dataM, RowSideColors = RowSideColors, ColSideColors=ColSideColors, main = title, margins = c(50,50), scale= do.scale ,labRow=geneNames, labCol=colLabels, col = hmcol, cex.main = 1, cexRow = row.lab.mag, cexCol = col.lab.mag) > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-29 r42686) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_U...

...ap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both"), scale = c("row"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(5, 10), xlab = "EXPRESSIONS", ylab = "GENES", labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c("none"), ) I have certain queries regarding the same. 1. why the heat map is totally different from what the sequence of information is? 2. Is there any way to arrange the data based on the expression pattern of the genes or some other way,...

...ied the following solution : heatmap.2(Matrix2, symm=T, breaks=20, col=rich.colors(19), main="Matrix2", density.info="histogram", denscol="black", Colv=z$Colv, Rowv=z$Rowv, trace="none", na.rm=T, keysize=1.5, dendrogram="none",labRow=labels(z$Rowv), labCol=labels(z$Colv)) But I still get the same problem of mismatch between labels and columns/rows as well as loosing the wanted order of labels in the image. I would appreciate any suggestions and help Shany [[alternative HTML version deleted]]

...adientMode=" Diagonal Edge", Rowv=TRUE, Colv=FALSE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale = c("column"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(03, 40), xlab = "", ylab = "", labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c("none"), ) Thanks in advance Kamal [[alternative HTML version deleted]]

...] 0 8 0 0 1 [2,] 0 160 0 0 2 [3,] 0 175 0 0 3 [4,] 0 253 0 0 4 [5,] 79 212 0 0 5 [6,] 6 105 0 0 6 and call: ##------------ Heatmap -------------- library(RColorBrewer) rc <- grey((nrow(x):1)/nrow(x)) heatmap(data.matrix(x[,1:4]), Rowv=NA, Colv=NA, scale='none',labCol=NULL, revC=TRUE, col = brewer.pal(9,'Greys'), ylab='time',margins=c(6,5), cexRow=1.5, cexCol=1.5, RowSideColors = rc) I end up with something like attached 'heatmap'. How can I change my call to: 1) most important: there are black strips on the right-hand side, the...

...;,"red"))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale = c("row"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(25, 20), #xlab = "" ylab = "" labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c("none") ) I am giving two color only i.e red and black but when I am try to make the plot it again show in gradients. Therefore, I just want to plot a heat map with two color scheme. Thanks in advance Thank you Khushwant [[alternative HTML...

...ot;red"))(256), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale = c("column"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(01, 55), xlab = "", ylab = "", labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c("none"), ) Thank you in advance K>S [[alternative HTML version deleted]]

...; "denscol" "density.info" [17] "di" "distfun" "hcc" "hclustfun" [21] "hcr" "hline" "iy" "key" [25] "keysize" "labCol" "labRow" "lhei" [29] "linecol" "lmat" "lwid" "main" [33] "margins" "max.breaks" "max.raw" "max.scale" [37] "min.breaks" "m...

...]] heatmap.2(ccc, breaks=c(-0.1,0,0.1,0.25), col=brewer.pal(3,"Blues"), Rowv=FALSE, Colv=FALSE,symm=TRUE, key=TRUE,symkey=FALSE, density.info="none", trace="none", cexRow=0.75, keysize=1, scale = "none", dendrogram="none",labRow=FALSE,labCol=FALSE, main='Total') #axis(2, labels=rlab) ### does not works gives error asking to supply values of at. I would appreciate any directions on this Thanks -- View this message in context: http://r.789695.n4.nabble.com/row-names-of-a-heatmap-on-left-hand-side-tp4426353p4426353.html Sent...

...nsibly. reorder.dendrogram() now results in a dendrogram with correct "midpoint"s, and hence reordered dendrograms are plotted correctly. stats:::midcache.dendrogram() and hence the reorder() and rev() dendrogram methods do not return bloated dendrograms. o heatmap(*, labRow=., labCol=.) now also reorders the labels when specified---not only when using default labels. o Copying lattice (grid) output to another device now works again (There were intermittent problems in 1.9.0 - PR#6915, #6947/8.) o hist() uses a more robust choice of its 'diddle' fact...

...nsibly. reorder.dendrogram() now results in a dendrogram with correct "midpoint"s, and hence reordered dendrograms are plotted correctly. stats:::midcache.dendrogram() and hence the reorder() and rev() dendrogram methods do not return bloated dendrograms. o heatmap(*, labRow=., labCol=.) now also reorders the labels when specified---not only when using default labels. o Copying lattice (grid) output to another device now works again (There were intermittent problems in 1.9.0 - PR#6915, #6947/8.) o hist() uses a more robust choice of its 'diddle' fact...

I would like to organize my data as follows: I have a table that contains various data, and the numbers represent a level of similarity between these data, eg RF00013 has 100% similarity with the data RF00014. I would leave my table as a heatmap where darker colors represent higher similarity, and the lighter colors represent less level of similarity. I'm using version 2.11 of R. these