similar to: Plotrix Trick

Dear All, Please see the code snippet at the end of the email. I am using the color2D.matplot in Plotrix to plot a matrix. It works great, but there are a few things I cannot figure out (1) the value of cex.axis in the code snippet does not seem to affect the final pdf at all (at least on my system, Ubuntu 9.10, plotrix and Cairo installed from cran). How do I specify the size of the axis ticks

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",

Hi Function sequence() repeatedly concatenates its output, and this is slow. It is possible to improve on the performance of sequence by defining myseq <- function(x){unlist(sapply(x,function(i){1:i}))} The following session compares the performance of myseq(), and sequence(), at least on my G5: > identical(sequence(1:50),myseq(1:50)) [1] TRUE > system.time(ignore <-

Hi Function sequence() repeatedly concatenates its output, and this is slow. It is possible to improve on the performance of sequence by defining myseq <- function(x){unlist(sapply(x,function(i){1:i}))} The following session compares the performance of myseq(), and sequence(), at least on my G5: > identical(sequence(1:50),myseq(1:50)) [1] TRUE > system.time(ignore <-

Hi all. I am having a problem using color2D.matplot I am trying to visualize several different matrices under two color ranges. One color range corresponds to values less than 1 and the second color range for values greater than 1. However, the minimum value of each matrix differs and is automatically set to have the smallest value in the color range. Similarly, the maximum value of each matrix

Hi, I have encountered this problem quite a few times and thought I would ask. Let's say that I have two endpoints, a and b, which are integers. If a <= b, I would like to get a:b, but if a > b, then numeric(0), for example: myseq(3,5) => 3:5 myseq(3,3) => 3 myseq(3,2) => numeric(0) The operator : just gives decreasing sequences in the latter case, and I could not coax seq

Last Friday, I noticed that it is difficult to work with regression models in which there are factors. It is easier to do the old fashioned thing of coding up "dummy" variables with 0-1 values. The predict function's newdata argument is not suited to insertion of hypothetical values for the factor, whereas it has no trouble with numeric variables. For example, if one uses a

Hello, everyone. I am trying to show the correlation matrix using color2D.matplot(). And I want to map (0,1) to (dark red to dark green). But by default color2D.matplot() will map(min element of given matrix, max element of given matrix) to (dark red to dark green). Can anyone help me with this issue? Thanks a lot! Youcheng Lin ____________ [[alternative HTML version deleted]]

I am using color2D.matplot to plot a matrix about 400 by 200. The values in the matrix are 0:5 and NA. The resulting plot is not color, but shaded b/w. I tried to figure out how to add colors, I would like something like c(blue, green, red, cyan, green) #example motifx <- matrix(NA, nrow=100,ncol=20) motifx[,1:5] <- 1 motifx[,6:10] <- 2 motifx[,11:15] <- 3 motifx[,15:19] <- 4

Hi guys of the R-Help-Team!<br /><br />First of all - you do a great job!<br />I've found a lot of your mails in the internet. So I thought it would be a good idea to ask you a question about R.<br /><br />R is new to me, so sorry, if the question is too simple :)<br /><br />I have a matrix.<br />I can make a 2D Heatmap of this matrix.<br

Dear all I am using color2D.maplot to map some matrixes to plot. everything works fine. It seems that when my matrix contains only the same value color2D.maplot returns the following error: color2D.matplot(estimatedsr,redrange=c(0,1),greenrange=c(0,.5),bluerange=c(0,.5),xlab="x",ylab="y",main=sprintf('Estimated'),show.legend=TRUE,show.values=TRUE) Error in rgb(reds,

Hello, I have a matrix A with value varying from -1 to 1. I hope to use scaled color based on its value to produce an image of this matrix. Suppose I hope to label those data in [-1,-0.5] with blue, label those [-0.5,0.8] with light blue (tone is proportional to its value, e.g. rgb(1-tone, 1-tone, 1) where tone=abs(A)/0.5), and label those [0.8,1] with white. How can I use image() and rgb() to

Dear all, I am trying to make a series of waffle plot-like figures for my data to visualize the ratios of amino acid residues at each position. For each one of 37 positions, there may be one to four different amino acid residues. So the data consist of the positions, what residues are there, and the ratios of residues. The ratios of residues at a position add up to 100, or close to 100 (more on

Dear R-help, Could any of you direct me to a function for plotting a grid of colours, directly specified by a matrix of hex colour codes? In other words I'm looking for a heatmap() or image()-like function to which I can specify the colour of each grid location directly, rather than providing a numerical matrix and a 1D-colour scale (heatmap, image, levelplots,NeatMap...). I'm surprised

Hi all, I have posted similar questions regarding this topic, but I just can't seem to get over the hump and find a straightforward way to do this. I have attached my file as a reference. Basically, the attached file is a 5 degree by 5 degree grid of the the world (2592 cells), most of them are NA's. I just want to be able to plot this grid over a world map and color code the cells. For

Dear R users, I have a 51 by 51 matrix of p-values (named as pvalue_MA). I want to present graphically this matrix in a plot (filled contour plot) where both axes represent probabilities. I have also added a grid in this plot. I want to highlight in white the cells of the grid that represent p-values smaller than the (common) significance threshold, 0.05. The code from this plot is colored in

Hello, I am an absolutely beginner with regards to R, so forgive me for my potentially very stupid questions. I have been attempting to create recurrence plots using R. The data I am using is based on a mutually exclusive and exhaustive coding scheme with over 40 individual codes which can be assigned to 6 higher order categories. When I carry out the usual rqa command, my plot is pretty much

Hello there! I'd just like to say in advance, "Thank you," for any help and/or advice. My problem is as follows: I have a dataset that is made up of percentages. I've assigned my "error" percentages a value of '-100', my "non-existent" percentages a value of '0', and all my other percentages are normal values that range from the high

Hi Peter, You didn't give a very specific example, but it seems to me that what you wish to do is not really complicated. I suppose you have created a table of sequences vs. say hyprophobicity, charge, etc..., something like... seq hydroph arom b0001 0.104762 0.000000 b0002 0.035122 0.065854 b0003 0.024193 0.070968 b0004 -0.096729 0.084112 b0005 -0.973469 0.091837 b0006

Hi, I have searched for a solution but I failed to find an answer. I am hoping you may be able to help me. I have a data set where I have observations for a number of units (n =~40) over a period of time (t =~100) and I have a variable (Z) that codes a categorical variable for each observation. I want to produce a 2D plot where time is on the x-axis and units are on the y-axis. Then each block