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I'm pleased to announce that the FuncMap (v 1.0) package is available on CRAN. This is a single function package that makes hive plots of function calls for a specified package. Hive plots are a powerful concept developed by Martin Krzywinski at the Genome Sciences Center (mkweb.bcgsc.ca/linnet/). FuncMap is a simple implementation of Martin's concept. Function calls in a package are categorized as source functions, sink functions, or middle-managers, and plotted on 3 axes with several options available (?FuncMap for details of course). I'm not entirely certain...

I am having problem installing the affycoretools package. When I do it through biocLite, I get error messages saying the package XML cannot be installed and that I need a more recent version of libxml2. When I try to install the tar.gz file, I get the message /usr/local/R/2.4.0/lib/R/bin/exec/R: error while loading shared libraries: libg2c.so.0: cannot open shared object ERROR: installing

http://r.789695.n4.nabble.com/file/n2548152/25jfmyx.jpg HOW to create image like this? **tp://i55.tinypic.com/25jfmyx.jpg[/IMG] I don't known how to create the image above or which function can create this image? -- View this message in context: http://r.789695.n4.nabble.com/HOW-to-create-image-like-this-tp2548152p2548152.html Sent from the R help mailing list archive at Nabble.com.

I'm pleased to announce that the FuncMap (v 1.0) package is available on CRAN. This is a single function package that makes hive plots of function calls for a specified package. Hive plots are a powerful concept developed by Martin Krzywinski at the Genome Sciences Center (mkweb.bcgsc.ca/linnet/). FuncMap is a simple implementation of Martin's concept. Function calls in a package are categorized as source functions, sink functions, or middle-managers, and plotted on 3 axes with several options available (?FuncMap for details of course). I'm not entirely certain...

Hi, I'm trying to save heatmaps as PDFs. However, the PDF version of the heatmaps (Heatmap_CAFvsTNF_run2.pdf) is blurred when compared to its counterpart, which was saved manually by using the software "Grab" (Heatmap_CAFvsTNF_run2.tiff). -----R code-------- sample_output <- "stroma_run2" filename <-

I'm fairly new to the silhouette functionality in the cluster package, so apologize if I'm asking something naive. If I run the 'agnes(ruspini)' example from the silhouette section of the cluster package vignette, and assign colours to clusters, two clusters have what appear to be incorrect colours in the silhouette plot. library(cluster) data(ruspini) ar<- agnes(ruspini)

Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance

I'm new to R and am trying to perform a simple, yet problematic task. I have two variables for which I would like to measure the correlation and plot versus each other. However, I have ~30 million data points measurements of each variable. I can read this into R from file and produce a plot with plot(x0, x1) but as you would expect, its not pretty to look at and produces a postscript

Hello, I'm trying to plot a historgram with a density plot superimposed: hist(x, seq(-1, 1, by = 0.1), prob = T, col = "blue") lines(density(x, bw = 0.1)) rug(x) I don't want to add rug(x) but the histogram will not be plotted unless rug(x) is there. It does not work if the "hist" line alone is present. Can you help? Thanks, Kim [[alternative HTML version

Hi all, I am a novice user of the heatmap.2 function in the Bioconductor gplots package. I am trying to create a heatmap diagram from a hierarchical clustering result based on the complete linkage and the pearson correlations as the distance metrics. After reading the help page for heatmap.2, it seems that it calls the distfun and hclustfun with the default settings. Is that the same as doing

I'm working on Human Exon Array 1.0 ST. I'm getting normalized data fine but I'm running into problems with QC. QCReport gives me the following error: > load(file= "huex10stv2cdf.rda") > exon.data at cdfName <- "huex10stv2cdf" > QCReport(exon.data, file = "QCReport.pdf") Error in as.vector(ans[[i]][, i.probes]) : subscript out of

Hi, I'm trying to plot bar graphs with stacked columns marked with askterisks for certain columns, which follow certain criteria. I've gotten the stacked bar plots with Data set A (please refer to code below). However, I haven't figured how to put asterisks on columns based on some extra information (such as "used/unused") as in Data set B i.e. asterisks at the

Hello, I've been trying to use R-2.11.1 but I get the following error when trying to run R on linux: "error while loading shared libraries: libRblas.so: cannot open shared object file: No such file or directory" How can I solve this problem? Best, Katy

I am doing an analysis that requires me to calculate correlations for a matrix of 15,000 rows x 50 columns. For each row I want to calculate the correlation to all other rows and then for each row, find the n (say 10) most correlated rows. If read in the 15,000 x 50 data from file and pass it to 'cor', this function quite appropriately (and very quickly) calculates all possible row by