similar to: heatmap.2 and three colours for specific ranges‏

Hi, i created a graph with heatmap(sma) function: heatmap(dataHeat(x)) and I wish to change the gradation of colors from blue to red, how could i do? Using "heatmap(dataHeat(x), col=c(2,4))" i will use only 2 colors without gradation. Ty so much Andrea

Hello all, I am using the heatmap.2 function in the gplots package. I want to supress the reordering of the columns of the data matrix i pass to the function. I used the statement, heatmap.2(z,Colv=FALSE,dendrogram="row",col=redgreen(75)) where z, is the matrix of data. The output i want should have the rows reordered along with the dendrogram and the columns should be in the original

Hi, I have a question about heatmap. I have a data with row as microRNA and two columns are two cell expression values for these microRNA. So, like: cell1 cell2 miRNA1 1.5 3.4 miRNA2 1.3 2.4 ................... miRNA50 5 2.1 miRNA51 7.3 0.5 I want to see some miRNA are high in cell1 and low in cell2 but others are low in cell1 and high in cell2. I

Dear all, I've been trying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following: library(gplots) dat<-cor(matrix(rnorm(100, m=10), nrow=10)) mat<-cor(matrix(rnorm(100), nrow=10)) dev.new() heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none",

Hello everybody, I'm trying to create my own color palette on R, in order to interpolate some different temperature data on different maps (daily means, seasonal means,...). I would like to create a color palette which works for each map, so I need a color palette between -40 and +40?C. Sometimes my data for one map range from -10 to +20, sometimes from 10 to 30, etc... but always between

Dear list I'm having trouble with inverting color gradation. As seen in the "rgl" example, library(rgl) example(rgl.surface) I understand that I can assign colors to heights for each point. col <- colorlut[ y-ylim[1]+1 ] # assign colors to heights for each point However, I am now trying to assign inverted colors. (top colored green, and bottom colored gray). Is there any

Hello: I have a tab delim file with 100 rows and 100 columns. I have numerical values in this table. What I want is to create an image color map with color gradation. my values range from -5 to 0. max value is 0. to acheive this, I need to convert my data.frame into matrix. I tried following : mydf <- read.table('mytable',sep='\t',header=T) mydf1 <- mydf[,2:100]

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,

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!

Hello, I am trying to create a heatmap that clusters based on a k-means scheme rather than a hierarchical clustering scheme. Suppose I have the following input data, located in sample.table: x1 x2 x3 x4 x1 17.198 16.306 16.806 16.374 x2 14.554 10.866 15.780 14.596 x3 14.374 14.118 14.569 17.352 x4 17.505 14.596 15.738 14.070 By using the heatmap.2 function as follows, I can create a heatmap

Hi, I am having troubles with heatmap(). I have a matrix containing pairwise distance values and I want to plot this matrix with heatmap. I wonder now what distfun is for. Is a distance matrix computed from my initial matrix again and then plotted? cheers, andreas

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'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

Hi , I am trying to plot a heatmap with a correlation matrix and trying to highlight significant correlations . i am using my matrix d874n has 78 columns ex2<-corAndPvalue(data.matrix(d874n),use = "pairwise.complete.obs") ##creating a matrix of true false using p values sig<-ex2$p<0.05 nx=78 ny=78 makeRects <- function(tfMat,border){ cAbove =

Hi, Can someone please guide me towards how to produce "heatmap" output from the output of "hclust" run prior to the actual "heatmap" call? I have some rather lengthy clustering going on and tweeking the visual output with "heatmap" recalculating the clustering every time is not feasible. Thanks, Joh

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 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

Using the heatmap.2 function, I am trying to generate a heatmap of a 2 column x 500 row matrix of numeric values. I would like the 1st column of the matrix sorted from the highest to the lowest values - so that the colors reflected in the first column of the heatmap (top to bottom) go from red to green. After sorting the matrix (z), I tried the following command, but the data remains

Hi, I am using the function heatmap(stats) to draw a microarray heatmap, columns are samples and rows are gene features. I did a 2D clustering during the heatmap drawing. The features and samples indeed cluster into several blocks both vertically and horizontally. I can get the index of re-ordered rows and columns after the heatmap drawing by typing the the return variable of the heatmap

Hi I made heatmap of QTL based on Lod score. Where I have traits in columns and marker data (rows). I can not cluster both column and rows as I need the right order for marker data. Can someone suggest me better way of generating heatmaps especially the colour key I want to select to visualize the results which are more interesting to look at. > library(gplots) >