search for: sepwidth

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 colu...

...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", 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 inform...

..., I'm trying to learn how to use lattice and levelplot in particular. There are three elements of customizing the plots I'm stuck with: a) Is there a way to put borders around each "cell" within a level-plot. I'm trying to do something like the colsep/rowsep/sepcolor/sepwidth parameters of heatmap.2 in gplots b) Can I alter the line-width of dendrogram added to the levelplot using latticeExtra? c) Can I alter the spacing between the dendrogram and a row of coloured rectanges added to a dendrogram using the add option? The basic code-example that I've been try...

I'm using this code to create a heatmap of expression data and indicate a specific column of data, post clustering: #Generate heatmap: heatmapChipDx <- heatmap.2(L3data_med2, dendrogram="column",trace="none", col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1, margin=c(5,5), scale="row", key=FALSE) I have two problems that I'm hoping i can get some pointers on: 1. The column I want to indicate with a yellow line is column #1 in the matrix, pre-clustering. How can I determine its position post-clustering, so I can instruct the heatm...

...red"))(256), #col=greenred(75), #col = cm.colors(256), #bgStyle="3D Rectangle", #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]]

...t;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 = 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 pl...

...RUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("green","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]]

...uot;nr" [49] "op" "retval" "revC" "rm" [53] "rowInd" "rowsep" "RowSideColors" "Rowv" [57] "scale" "scale01" "sepcolor" "sepwidth" [61] "sx" "symbreaks" "symkey" "symm" [65] "tmpbreaks" "trace" "tracecol" "vline" [69] "x" "xlab" "x.scaled" "x.u...

...heatmap of expression data and > indicate a > specific column of data, post clustering: > > #Generate heatmap: > heatmapChipDx <- heatmap.2(L3data_med2, > dendrogram="column",trace="none", > col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1, > margin=c(5,5), scale="row", key=FALSE) > > I have two problems that I'm hoping i can get some pointers on: > > 1. The column I want to indicate with a yellow line is column #1 in > the > matrix, pre-clustering. How can I determine its position post- &g...