similar to: intensity map / plot

Hi, I am still struggling with three dimensional arrays. Now I would like to convert a three dimensional array into a data-frame with the coordinate-columns: x, y, z and a value-column. And I definitely don't want to loop over every element, since this would be very resource intensive for the actual data-set. Are there any specific functions that are helpful for this task?

Hi, I try to create PNG images of a certain size where each pixel intensity corresponds to exactly one probe signal in an Affymetrix array. I try to use png() and image() with zero margins to do this. Example: z <- matrix(1:15, nrow=45, ncol=30) png("large.png", height=nrow(z), width=ncol(z), bg="red") par(mar=c(0,0,0,0)) image(z, col=gray.colors(16), axes=FALSE)

Dear R-experts, I have found a splom-modification online which is given below. This works perfectly, but I would like to have a matrix of given correlation values to be used in the lower triangular part (lower.panel) of the splom-plot instead of calculated correlation values. Here is the matrix I would like to use (it can be any other convenient data structure):

Hi, is there a way to place text at the upper left corner (or another corner) of the plot? I want to place it really at the upper left corner of the whole plot (the file I get), not at the upper left corner of the plot-region. I tried text() and mtext(), and corner.label() of the plotrix package but it didn't work out. thanks!

Hello, I am trying to download a SOFT matrix file for GSE series to extract raw intensity data. gse<- getGEO('GSExxxx', AnnotGPL=T) However, I am not able to use the function Table(gse), which returns the following error >>>Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Table", for signature "GSE" If I

Full_Name: Jae Choi Version: 1.6.1 OS: linux (x86) Submission from: (NULL) (142.176.61.245) Hello, Any attempts to access the "hsv" function returns the following type of error: Error in hsv(h = seq(start, ifelse(start > end, 1, 0) + end, length = n)%%1, : color intensity 1.25, not in [0,1] (the above was generated from the demo command: > pie(rep(1, 24), col =

Hi again, Thanks Ted and Marc its works. But of course after pulling in in some real life data I discoverd one hitch. Often there are missing intervals. For example: from <- c(0, 1.2, 4.0, 4.2, 5.0, 25.0, 30.1, 45) to <- c(1.2, 4.0, 4.2, 5.0, 25, 30.1, 36.2, 50) intensity <- c(0, 1, 3, 2, 1, 0, 2, 5) barplot(intensity, width = -(to - from), space = 0, horiz = TRUE, ylim =

Hello, I have a question about how to plot a series of data. The folloqing is my data matrix of n > n 25p 5p 2.5p 0.5p 16B-E06.g 45379 4383 5123 45 16B-E06.g 45138 4028 6249 52 16B-E06.g 48457 4267 5470 54 16B-E06.g 47740 4676 6769 48 37B-B02.g 42860 6152 19276 72 35B-A02.g 48325 12863 38274 143 35B-A02.g 48410 12806 39013 175 35B-A02.g 48417 9057 40923

Dear all, I have tried to plot a triangular matrix with the function persp3d(rgl). for example z=rbind(c(1,NA,NA,NA),c(5,3,NA,NA),c(4,2,9,NA),c(8,6,5,11)) x=1:4 y=1:4 persp3d(x,y,z,color="gray") The two extreme points are not plotted (value=1 and value=10). It seems because the half of the matrix have 'NA' and perp3d need planar quadrilateral face. So I decided to use the

Hi all, I'm trying to visualize animal movement data characteristics spatiotemporally by overlaying many different histograms on a map. I want the histograms to be plotted at coordinates in the map that matches a region they describe. If I was just doing this once, I'd fiddle in Illustrator after R and avoid the headache. But I'll be doing it many many times so it seems

code: op <- par(bg='black',fg='gray',col='gray',col.axis='gray',col.lab='gray',col.main='gray',col.sub='gray',mai=c(0,0,0,0), tck = 0.01, mgp = c(0, -1.4, 0), mar=c(0,0,0,0)) plot(x,y,ylim=c(-20,20),xlim=c(min(x),max(x)),pch='X',col = rgb(1,1,1, 0.5),yaxt="n", ann=FALSE) abline(v=c(min(x),max(x)), lty=3,

To anyone who can help me: I found that the function "smooth.ppp" in the package "spatstat" provides the kernel estimate for the intensity function of a "two-dimensional" point process with marks. Does anyone know that which package can do this for simply a "one- dimensional" point process with marks? I've been searching all over the R site but still

Hi, I am facing a problem with the legend, I don?t know how to use the fill option in the legend in order to achieve the same standard gray levels that are plotted. Sorry for this easy one, but I really did not find anything so far. It works fine with color: ###### C O L O R mat <- matrix(2,3,rep(2,6)) rownames(mat)<-c("A","B","C") par(xpd=T,

Hi, Is there any way to plot a Map with different shading patterns, instead of color intensity, in R2.0.1 over Linux ? Thanks. D ----------------------------------------- Stay ahead of the information curve. Receive GIS news and jobs on your desktop daily. Subscribe today to the GIS CafeNews newsletter. [ http://www10.giscafe.com/nl/newsletter_subscribe.php ] It's informative and

Hello R-helpers I want to put a color scale in a plot: I've got an xy plot where the values of the response (z=f(x,y)) is symbolically given by colors (like heat or rainbow color scale) I would like to put such a scale with apprpriates labels in the plot, so as to facilitate the interpretation (like in a finite elements result plot) How is taht possible? Thanks Anne [[alternative

Dear colleagues, I have an image which I can display in the greyscale using image. On this image, for some pixels, which I know, I want to display their activity based on a third measure. One way to do that would be to color these differently, and use an opacity measure to display the third measure. An example of what I am trying to do is at:

If I have a contourplot (in the lattice package) and I want to add straight lines to it, how do I do this? I see that there are llines() and lsegement() functions for lattice plots, but they don't seem to do anything in this case: library(lattice) library(KernSmooth) x=rnorm(10000) y=x+rnorm(x,0,.5) a=bkde2D(cbind(x,y),.7) z=as.vector(a$fhat) grid=expand.grid(x=a$x1,y=a$x2) grid$z=z

Hi, I'm trying to draw a 2D plot using multiple tints of red. The (simplified) setup is the following: || year | x | y || My idea is that each year is plotted with a different tint of red. Older year (lightest) -> Later year (darkest). I've managed to plot this with different scales of grays simply by doing: palette(gray(length(years):0/length(years))) before the plot and for each

Hello again, I am trying to create a color scale plotting the hydroathy index (y-axis) versus residue (x-axis) - each residue (1-100) has a value between 0-1. I've been trying to create a scale where: 0-0.499: increasing intensity of red 0.5- yellow 0.51 - 1 increasing intensity of green. THis is in lieu of a line graph. I'm not sure which type of plot to begin with - I attempted to

Hi, I'm trying to make a png file of a histogram. I would like a white background in the final product but end up producing a gray one, despite setting what I think are the correct parameters. Suggestions for how to properly set a white background would be welcome. Thanks in advance, Scot # for non-lattice > par("bg"="white") > par("bg") [1]