search for: rowind

...norm(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) Platform: x86_64-pc-linux...

...4-17) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 # The correct results > hv <- heatmap.2(x, col=col.palette, Colv=FALSE, key=TRUE, Rowv=cc1$order, dendrogram="row", scale="none", tracecol="white", cexCol=.5) > hv$rowInd [1] 26 23 5 19 15 4 2 16 21 13 22 12 10 20 7 3 25 1 8 11 24 9 18 14 17 [26] 6 # Attempt 1 > cc = as.dendrogram(hclust(dist(x))) > hv1 <- heatmap.2(x, col=col.palette, Rowv=cc, Colv=FALSE, key=TRUE, dendrogram="row", scale="none", tracecol="white&q...

...ument does not solve the problem: heatmap(cU, symm = TRUE, distfun = function(c) as.dist(1 - c), ColSideColors=sideCols, RowSideColors=rev(sideCols)) I had a look at the the function code and found that this change fixes the problem: Replace image(rbind(1L:nr), col = RowSideColors[rowInd], axes = FALSE) with image(rbind(if(revC) nr:1L else 1L:nr), col = RowSideColors[rowInd], axes = FALSE) I am using the current version of R for Mac OS X: > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF...

Hello all, I am trying to sort rows of one matrix by rows of another. Given a1 and a2: ------ > a1 [,1] [,2] [,3] [1,] 7 6 8 [2,] 4 2 4 [3,] 4 7 2 [4,] 0 3 8 a1 <- structure(c(7, 4, 4, 0, 6, 2, 7, 3, 8, 4, 2, 8), .Dim = c(4L, 3L)) > a2 [,1] [,2] [,3] [1,] 101 102 103 [2,] 101 102 103 [3,] 101 102 103 [4,] 101 102 103 a2 <-

Hi All, I have a matrix like m <- matrix( letters[1:10], ncol=5) How to conver it to 10 * 3 matrix, which the first col is row index of m, second col is colum index of m and third column is the value of matrix, say 1 1 1 "a" 2 1 2 "c" 1 3 "e" etc... Thanks. [[alternative HTML version deleted]]

...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. Code from heatmap(), R 1.8.1: x <- x[rowInd, colInd] if (is.null(labRow)) labRow <- if (is.null(rownames(x))) (1:nr)[rowInd] else rownames(x) if (is.null(labCol)) labCol <- if (is.null(colnames(x))) (1:nc)[colInd] else colnames(x) ... axis(1, 1:nc, labels = labCol, las = 2, line = -0.5, tick = 0,...

...col(lmat)) op <- par(no.readonly = TRUE) on.exit(par(op)) layout(lmat, widths = lwid, heights = lhei, respect = FALSE) if (!missing(RowSideColors)) { if (!is.matrix(RowSideColors)){ par(mar = c(margins[1], 0, 0, 0.5)) image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE) } else{ par(mar = c(margins[1], 0, 0, 0.5)) rsc = RowSideColors[rowInd, ] rsc.colors = matrix() rsc.names = names(table(rsc)) rsc.i = 1 for (rsc.name in rsc.names) { rsc.colors[rsc.i] = rsc.name...

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

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

...nitial heatmap, with all 1000 rows and write it to an object 'heatAll' heatAll = heatmap.2(combined.int.top, col = cm.colors(256), trace = "none") pdf(file="~/Desktop/Alfalfa-Ladak-StemV3.pdf", width=8, height=12, pointsize=4) for(i in 1:20){ selected = heatAll$rowInd[((i-1)*50):((i-1)*50+50)] ##get original row order in groups of 50 heatmap.2(combined.int.top[selected,], Rowv = FALSE, ##prevent row re-ordering Colv=heatAll$colInd, col=cm.colors(256), trace="none", margins = c(9,8), main=paste("page", i, sep=" "))...

....9 30773.4 32918.6 34412.1 33954.6 [10,] 36.3 69.8 92.0 52.0 57.3 64.9 Also, is it possible to get the order in which the rows will be clustered , starting with the first rows joined into a group and then followed by other grps added. I thought i could extract the order by using $rowInd, but looks like it's the order in which the rows are reordered in the map. Please let me know how to do this. Thanks, Vasu. [[alternative HTML version deleted]]

...ng hierarchical clustering and display the results in the form of a heat map. In a Heat map, is it possible to get the order in which the rows will be clustered , starting with the first rows joined into a group and then followed by other groups added. I thought i could extract the order by using $rowInd, but looks like it's the order in which the rows are reordered in the map. Also, is it possible to add a color key to the heatmap, similar to the one displayed in a level plot. Thanks, Vasu. Research Graduate Student Bioinformatics Research Group UofL, KY [[alternative HTML version deleted...

..."na.color" "na.rm" "nbr" "nc" [45] "ncol" "notecex" "notecol" "nr" [49] "op" "retval" "revC" "rm" [53] "rowInd" "rowsep" "RowSideColors" "Rowv" [57] "scale" "scale01" "sepcolor" "sepwidth" [61] "sx" "symbreaks" "symkey" "symm" [65] "tm...