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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) %||%

Hi, I am trying to create a heatmap with some specific requirements. Specifically, I need to be able to center the color-scale around 0, and I need to truncate the data so that a few extreme values do not cause the rest of the heatmap to appear black (on a red/green scale). After reading through and experimenting with heatmap, heatmap.2, heatmap_plus, and heatmap_2, I believe heatmap.2 will

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem: cU <-

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]]

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 original order.

Hello again, lately I have been playing a lot with heatmap functions, in particular I complemented heatmap.2 with a nice feature from heatmap.plus, i.e. the possibility of assigning a matrix to ColSideColors so to take into account more annotations. Below is the code I introduced in heatmap.2, everything else is maintained equal to heatmap.2: if (!missing(ColSideColors)) { #if

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

Hi All, I've worked on some code to take a heatmap with 1000 row entries, and split this up into 20 pages, each with 50 rows from the original heatmap. I want to preserve the row order such that all 20 pages, if put together, would comprise the original heatmap. Here's what I've done: ##make the initial heatmap, with all 1000 rows and write it to an object 'heatAll'

Hi all, I am trying to produce a heatmap to display clustering of similar rows in the data given below. For each given row, different colors are used to represent the corresponding column value. I want to display the values of the colors in the form of a color key added to the heatmap. Is there anyway of doing this? > z[1:10,1:6] [,1] [,2] [,3] [,4] [,5] [,6] [1,]

Hello all, I am trying to cluster similar rows of a data matrix together using 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

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