search for: geneplott

On Tue, 18-Dec-2007 at 11:21AM -0500, James W. MacDonald wrote: |> Duncan Murdoch wrote: |> > Yes, I agree. (As an aside, there's actually a capital S in |> > smoothScatter(), and it's a bit of a pain to install, because |> > geneplotter depends on something that depends on DBI, which is not so |> > easily available these days.) |> |> Somehow I always forget the capital S and wonder if I have loaded the |> correct package ;-D Maybe you're misled from the output when the package is installed: >>> Bu...

...SQLForge 11: Biobase - An introduction to Biobase and ExpressionSets 12: Biobase - Bioconductor Overview 13: Biobase - esApply Introduction 14: Biobase - Notes for eSet developers 15: Biobase - Notes for writing introductory 'how to' documents 16: Biobase - quick views of eSet instances 17: geneplotter - How to assemble a chromLocation object 18: geneplotter - Visualization of Microarray Data 19: xtable - xtable Gallery Selection: 17) Opening /home/lbthrice/R/i486-pc-linux-gnu-library/2.8/geneplotter/doc/byChroms.pdf > Couldnt get a file descriptor referring to the console Could not get a...

Hello R help list I have been using the smoothScatter function within the "geneplotter" package to make some graphs using a Sweave Rnw script called via Rscript in a DOS/Windows batch file. The Rscript will ultimately be called by a web service with time-out constraints, hence things need to run as swiftly as possible. The geneplotter package is currently loaded each time R...

Hi, I have been trying to plot density plots using the example on: http://addictedtor.free.fr/graphiques/graphcode.php?graph=139 I used to use this function, but I cannot get any old code or even the example to work. library("geneplotter") require("RColorBrewer") x1 <- matrix(rnorm(1e4), ncol=2) x2 <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2) x <- rbind(x1,x2) layout(matrix(1:4, ncol=2, byrow=TRUE)) op <- par(mar=rep(2,4)) smoothScatter(x, nrpoints=0) smoothScatter(x) smoothScatter(...

Hi, I have a set of genes and its chromosomal physical position in a text file. I want to view those genes in the chromosome using R package GenePlotter. Could any one please tell how to view this. Thanks in advance. Yours sincerely, S.Mahalakshmi [[alternative HTML version deleted]]

...file for hgu95av2 assembled using data from public data repositories Maintainer: Lin,Chenwei < clin at fhcrc.org > LazyLoad: yes Depends: R(>= 2.0.0) License: LGPL Packaged: Thu Mar 3 15:43:00 2005; biocbuild It is an example database of the geneplotter library. Trying to install, I got: $ R CMD INSTALL hgu95av2_1.7.0.tar.gz * Installing *source* package 'hgu95av2' ... ** R ** data ** preparing package for lazy loading Error: 'delay' is defunct. Use 'delayedAssign' instead. See help("Defunct") Execut...

...f, and want this light blue "range" to extend throughout the entire area of the resized plot. I have attempted to add NAs, but it has no effect on expanding this light blue plot area. Code is below. #### xyz is a dataframe containing two columns with corresponding x and y values library(geneplotter) library(RColorBrewer) layout(matrix(1:1, ncol=2, byrow=TRUE)) smoothScatter(xyz, nrpoints=0, xlim=c(-3,3), ylim=c(0,5),colramp=colorRampPalette(c("#f8f8ff", "white", "#736AFF", "cyan", "yellow", "#F87431", "#FF7F00", "r...

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

...nductor version 2.6 packages: [1] "affy" "affydata" "affyPLM" "affyQCReport" [5] "annaffy" "annotate" "Biobase" "biomaRt" [9] "Biostrings" "DynDoc" "gcrma" "genefilter" [13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma" [17] "marray" "multtest" "vsn" "xtable" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '\Users\dbickel/R/w...

...matrix A which looks like this: ,1 ,2 ,3 ,4 1, 1 10 100 1000 2, 0.5 0.2 1.0 4.3 3, 0.1 0.2 0.3 0.5 ..... where the 1st row is representing the X-axis values. The subsequent rows should be plotted on the y-axis. I would prefer to use the smoothScatter plotting function of the geneplotter package, but to begin with R I'd be happy to use any scatterplot with the given dataset provided in the matrix A. So I tried: plot(A[1,],A[2:3,]) or plot(A[1,],A[2-3,]) both result in : Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ Wh...

Hello, I am searching for the best method to plot two variables with points whose output color depends on the size of a third variable. For example, the darkness of the x-y point would increase incrementally based on the size of the z value, similar to the colramp parameter in geneplotter. This would be analagous to symbols(), except changing the selection from the color gradient rather than the size of the plotted shape. The closest I have come so far is the levelplot() function, as below: graphdata <- alldata[,c("x","y", "size")] levelplot(size...

...C_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "datasets" "utils" [7] "methods" "base" other attached packages: geneplotter lattice annotate Biobase graph "1.14.0" "0.15-4" "1.14.1" "1.14.0" "1.14.2" [[alternative HTML version deleted]]

...tall the following packages: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" Anything that I install after this gives me the same error...

...tpext.usgs.gov/pub/er/fl/st.petersburg/Monica_pal/ The file is: robcor_training_pca.pdf - i will also attach this file in case some people accept attachments. So i took apart the cor.plot function from mvoutlier and i used instead of the scatter plot function the smooth scatter density plot from geneplotter, generating my own function called cordens.plot. Now i would like to add a colorbar on the right side of the graph with red as my highest density and purple as the lowest density and right next to the colors labels "min" for purple and "max" for red (i don't want actual nu...

...IME=English_United States.1252 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [9] "base" other attached packages: Rgraphviz geneplotter XML GOstats Category hgu95av2 KEGG multtest xtable "1.11.9" "1.11.8" "0.99-8" "1.6.0" "1.4.1" "1.12.0" "1.8.1" "1.11.2" "1.3-2" RBGL...

...nder development (unstable) (2006-01-04 r36984) powerpc-apple-darwin8.3.0 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: geneplotter annotate Biobase gplots gdata gtools "1.9.5" "1.9.2" "1.9.4" "2.0.0" "2.0.0" "2.0.0" RdbiPgSQL RdbiPgSQL Rdbi seanlib limma "1.0.9" "1.0.9"...

...-darwin6.8 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: convert seanlib gplots gdata gtools geneplotter annotate Biobase marray limma firstlook "1.1.9" "1.0" "2.0.0" "2.0.0" "2.0.0" "1.4.3" "1.5.1" "1.4.22" "1.5.24" "1.8.1" "...

hi, there: i have 2 questions associated with heatmap in heatmap.2{gplot}, there is a bar called "raw z-score" showing the coloring legend for each pixel. Where can I find that z-score's formulae? question 2, for example, I have 5 groups and I want to label each group with a color name from "#FF0000" to "#0000FF" evenly. so basically i need a vector like this:

dear all, I am writing a sweave documentation for my analysis, and I am plotting huge scatter plot data for microarray. unlucly this take a lot of resource to my pc because of the quality of the image which is to high (I see the PC get stuck for each single spot). how can I overcome this problem? is there a way to make lighter image? john [[alternative HTML version deleted]]

Dear all, I am running something similar to this short example: library("lattice") library("geneplotter") X=matrix(cbind(1:100,100:1,c(1:50,50:1)),ncol=3) Y=matrix(cbind(1:100,1:100,1:100),ncol=3) names=1:3 dummy.df = data.frame(names = factor(names, levels = names), x = seq_along(names), y = seq_along(names)) xyplot(y ~ x | names, dummy.df, xlim = c(1,100), ylim = c(1,10...