similar to: Flipping a heatmap

In using cor(data.frame), it is annoying that you have to explicitly filter out non-numeric columns, and when you don't, the error message is misleading: > cor(iris) Error in cor(iris) : missing observations in cov/cor In addition: Warning message: In cor(iris) : NAs introduced by coercion It would be nicer if stats:::cor() did the equivalent *itself* of the following for a data.frame:

I have a file of the following form -11 -10 -9 -8 -10 -9 -8 NA -9 -7 NA NA -8 NA NA NA So basically a NxN matrix of log scores. I want to get a heatmap of these log scores but I'm having a problem. I'm using the following code library(gplots) data=read.table("filein.txt",header=FALSE) mat=as.matrix(data) heatmap.2(mat,dendrogram=c("none")) But on the

Using the heatmap function in mva, it seems to be hard to use different colors in the edges leading to different groups of objects, as commonly done in many heatmaps in the microarray graphics. Any suggestions? Thanks. max

Hello all, I'm trying to create a heatmap using 2 matrices I have: z and v. Both matrices represent different correlations for the same independent variables. The problem I have is that I wish to have the values from matrix z to be represented by color intensity while having the values from matrix v to be represented by circle size. I currently have the following in front of me and an unsure

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

Hi, I'm kinda new of the R world. I need to use the heatmap or heatmap.2 function to plot correlation values. 2 questions: - how can I specify a color palette? (would like to have a transition from blue(-1) to white(0) to red(1)) - how can I use heatmap.2 imposing a specific order (like hclust.order)? I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to plot them

I'm having a problem when using heatmap. Even though the diagonal of my matrix is all the same value, the diagonal of my heatmap is not all the same color. Any suggestions? Here is some reproducible code: ######################################### # Get data nba <- read.csv("http://datasets.flowingdata.com/ppg2008.csv", sep=",") # Reorder nba <-

Dear R community! I am trying to create a heatmap based on the following data. As you can see the diagonal (0,0 to 10,10) is always 0). If I run the heatmap command like i posted it I get a graph with horizontal lines. What is my mistake? > heatmap(activity.matrix, Rowv = NA, Colv = NA, scale="column", xlab="x Compounds", ylab="y Compounds",

> I am trying to produce a heatmap of pairwise correlations, but since the matrix is > symmetric, I only need either the upper or the lower triangle. I have scoured the > web and R documentation, but I have not been able to find a way to produce such a > figure. Is there a simple way to produce a heat map with only the part above or > below the diagonal? You might want to check

Hi Kevin, >>>>> "krc" == krc <krc at odin.mdacc.tmc.edu> >>>>> on Mon, 27 Jun 2005 21:55:37 +0200 (CEST) writes: krc> Full_Name: Kevin R. Coombes krc> Version: 2.1.0 krc> OS: Windows XP krc> Submission from: (NULL) (143.111.224.169) krc> When revC = TRUE and RowSideColors is set to a list of krc>

I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: ------------ > dim(as.matrix(data.dcpm)) [1] 15462??? 18 > > heatmap(as.matrix(data.dcpm), col=topo.colors(100)) > heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE,

The question is how to use a URL in place of a file= argument for read.*.functions that do not support this internally. e.g., utils::read.table() and her family all support a file= argument that can take a URL equally well as a local file. So, if I have a file on the web, I can equally well do > langren <- read.csv("langrens.csv", header=TRUE) > langren <-

How can I read a space-delimited file, where the data values for each case are folded before column 80, and so appear on two lines for each case? The first few cases look like this loc type bio H2S sal Eh7 pH buf P K Ca Mg Na Mn Zn Cu NH4 OI DVEG 676 -610 33 -290 5.00 2.34 20.238 1441.67 2150.00 5169.05 35184.5 14.2857 16.4524 5.02381 59.524 OI DVEG 516 -570 35 -268 4.75 2.66 15.591 1299.19

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, I have a question about the heatmap dendrogram in R. I loaded my data matrix in command heatmap(), and it gave me a heatmap accordingly, and the rows (genes) also were clustered accordingly. But now I don't want the genes clustered in that way, I have a new order of these genes, and want the rows of the heatmap are drawed as the order I give. Could anybody help me on that? Thank you!

Hi Sorry to revisit an old problem, I seemed to solve this in 2004, only for it to resurface :-S I am trying to plot a heatmap, and I don't want the columns of my matrix re-ordered. The function doesn't seem to behave as the help would have you believe: a <- matrix(rnorm(100),nr=20) a.d <- dist(a) a.hc <- hclust(a.d) a.de <- as.dendrogram(a.hc) # columns are re-ordered

Hi, I was trying to use par(mfrow) to put 4 heatmaps on a single page. However, I get one plot per page and not one page with 4 plots. What should I modify? Test code is given below: test = matrix(rnorm(60), 20, 3) pdf(file='test.pdf',width=10,height=8) par(mfrow=c(2,2)) heatmap(test) heatmap(test) heatmap(test) heatmap(test) dev.off() thanks! [[alternative HTML version deleted]]

Hi, I have what would seem to be a very simple problem but have been unable to find any way to go about solving it: I am using heatmap.2 to create a heatmap and by default the x axis label is at the bottom of the heatmap, I simply want to move the label to the top of the heatmap. Any help with this would be greatly appreciated. Thanks, Mark

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

Howdy, I am trying to make a simple monochrome heatmap from 1 row of data. Essentially, I just want a long bar where black represents the max value in the data, white is the minimum, and all values in between are interpolated appropriately. I have tried using heatmap and heatmap.2, but both have issues. heatmap seems to be restricted to only drawing a square plot, and this data requires a