search for: labrow

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...

...): 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)[rowInd] labCol <- labCol[rowInd] %||% colnames(x) %||% (1L:nc)[colInd] Maybe this should be: labCol <- labCol[colInd] %||% colnames(x) %||% (1L:nc)[colInd] > sessionInfo() R Under development (unstable) (2020-06-21 r78727) Platf...

...ushViewport(viewport(layout.pos.col=1)) viewport[GRID.VP.178] > par(omi=gridOMI(),new=T) > my.heatmap(eb$coefficients[(clsum[,1]>1) & (clsum[,2]>1) & (clsum[,3]==0),],breaks=c(seq(-2.5,-0.6,0.1), -0.1,0.10,seq(0.6,2.5,0.1)),dendrogram="none",Colv=c(9:12,5:8,1: 4),labRow=rep('',520),margin=c(10,5),colsep=c(4,8),trace="none",density. info="none",col=greenred.colors(40),key=F) > popViewport() viewport[GRID.VP.177] > pushViewport(viewport(layout.pos.col=3)) viewport[GRID.VP.179] > pushViewport(viewport(layout = grid.layout(3, 1...

...t I am aiming to do and why "heatmap" and "image" functions don't work for me. Thanks in advance for your help. # Example: Suppose Z had 3 values (0,1,2) and I had 8 observations. hitmep <- matrix(c(0,2,1,0,2,1,1,0),2,4) # Graph 1: heatmap(hitmep2, Rowv =NA, Colv =NA, labrow =NULL, scale ="none") # Graph 2: image(t(hitmep2), axes =FALSE) # I like the layout of the plots. My problem with these is that I don't want Z's values (0,1,2) to have colors on a scale. I want to specify, for example, 1="blue", 2="yellow" and 3="green&qu...

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 co...

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 -15 to 5, as a result, the zero of z distribution are are either green region or red region of th...

...e 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 them readable). Do you have any suggestions to improve the labeling? I am thinking about using multiple columns to label the row names instead of one column(the default in heatmap.2). I have tried to use "mtext" to...

...probability space 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?...

...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, 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...

...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", 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 s...

...correct.method = "pmonly", summary.method = "medianpolish") ### genes with highest variation library(hgu133plus2.db) rsd <- apply(exprs(x), 1, sd) sel <- order(rsd, decreasing = TRUE)[1:250] u<-mget(row.names(exprs(x)[sel,]),hgu133plus2SYMBOL) heatmap(exprs(x)[sel, ], labRow=u) ### in this case it works to extract the gene symbol ### limma contrasts design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3))) colnames(design) <- c("control", "three", "six") fit <- lmFit(x, design) meanSdPlot(x) contrast.matrix <- makeContrasts(t...

...col4 etc.) I've tried 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]]

...le", #bgGradientMode=" 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]]

...orientation; replace 'time' label on the left side 4) put frame around the plot ##----------------- Heatmap2 ----------------- I did not try with ggplot, but tried with 'heatmap.2': heatmap.2(data.matrix(x[,1:4]), Rowv=NA, Colv=NA, dendrogram='none', scale='none', labRow=FALSE, cexRow=1,cexCol=1, col = brewer.pal(9,'Greys'), density.info='none', key.size=1, trace='none') and got heatmap2 attached if heatmap.2 is something you suggest, then the same questions apply + one more: 5) how to change 'Color Key' label and put it...

...quot;black","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 [[al...

...white","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]]

...; "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" "min.raw" "m...

...names(ccc)[[1]] 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-tp4426353p44263...

...9; more sensibly. 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...

...9; more sensibly. 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...