similar to: venneuler() - customize a few things.

Dear UseRs and DevelopeRs It would be helpful to see the color palette available in the venneuler() function. The relevant par of ?venneuler states: "colors: colors of the circles as values between 0 and 1" -which explains color specification, but from what pallette? Short of trial and error, i'd really appreciate if some one could help me locate a "0 - 1" pallette

I was wondering if anyone could help me figure out how to make a Venn diagram in R where the circles are scaled to the size of each dataset. I have looked at the information for venn (in gplots) and vennDiagram (in limma) and I cannot seem to figure out what parameter to change. I have looked this up online and do not seem to be seeing anyone else who has posted this question or the answer to it

Hi Dimtris and esteemed useRs, I don't understand why i get this error message when attempting to use merge() - > temp <- merge(x, y[,17, drop=FALSE], by=rownames, sort=FALSE) Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any' It should work because: > all(rownames(x[order(rownames(x)),]) == + rownames(y[order(rownames(y[,17,

Esteemed R-users, heatmap.2() is yielding an inappropriate key based on my colors and break-points. In the reproducible example below, the key is inappropriate (to me) because- 1. 'Orange' is simply not represented in the key, despite its prescence in the heatmap. 2. The proportions of the key are clearly out, ie., my largest bin, (0.1 - 0.2) is half the range, but this bin (colored

Hi, I was wondering if it would be possible to print the counts of common items in the venneuler() diagrams. Anybody knows a straightforward idea? I can always count things from the data matrix, but I have vectors with 50 thousands elements. thanks Francesco -- -------------------------------------- *Francesco Lescai, PhD* Research Associate in Genome Analysis Faculty of Biomedical Sciences,

Esteemed useRs and developeRs, I need to create a '3D line plot' (proper name?) of which an excellent example can be viewed here: http://cococubed.asu.edu/images/87a/images/unknown_pleasures.jpg I have some experience using the rgl package to create 3D PCA plots, but have no idea where to start for an image like this. I'd really appreciate suggestions & help on how might

Esteemed UseRs and DevelopeRs, Apologies if this question belongs else where, but it does concern R's package installation/maintenance. How does one start R within Emacs/ESS with root privileges? I tried without success: > M-x sudo R Why i'm motivated to do so: It seems logical to me, as the only user of the PC, to keep my R library consolidated in the universal library rather

Esteemed UseRs, This must be embarrassingly trivial to achieve with e.g., melt() and cast(): deduplicating records ("pw.X" in example) for a given set of responses ("cond.Y" in example). Hopefully the runnable example shows clearly what i have and what i'm trying to convert it to. But i'm just not getting it, ?cast that is! So i'd really appreciate some ones

Esteemed R Users, Would some one be patient enough to explain the variation i see when creating .pdf file output for my plots? FYI- my goal is produce the highest quality .pdf output from the R 'command line' as opposed to using the menu of the acitve graphics window. Im using 32bit WinXP. Session info at the bottom. I have Ghostscript v8.71 installed and in the Path such that

Dear r-helpers, Here I would like to have your kind helps on generating Venn diagram. There are some packages within R on this task, like venneuler, VennDiagram, vennerable. But, vennerable can not be installed on my Mac book. It seems VennDiagram can not work on my data. And, venneuler may have generated a wrong Venn diagram to me. Do you have any experience/expertise on those Venn diagram?

Esteemed useRs and Devs, Attempts to update package:rJava to the latest version have failed. See my code and output below. Notably, as suggested here http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing $ sudo apt-get install r-cran-rjava ran successfully without error or warning, but my rJava package is not updated, and remains un-updatable... Greatly appreciate any

Hi all, I am taking this over from r-help (see http://permalink.gmane.org/gmane.comp.lang.r.general/273985). I experience a segfault when calling gplots::heatmap.2(), but only when certain other packages are loaded. I am not sure for the correct place to send this bug report. Should I send it to the package maintainers directly? If R-help is the wrong place, please feel free to direct me to

Hi all, I experience a segfault when calling gplots::heatmap.2(), but only when certain other packages are loaded. I am not sure for the correct place to send this bug report. Should I send it to the package maintainers directly? If R-help is the wrong place, please feel free to direct me to the correct one. I am on debian (testing) linux 64 with the binary R distribution from the

Hi all, I experience a segfault when calling gplots::heatmap.2(), but only when certain other packages are loaded. I am not sure for the correct place to send this bug report. Should I send it to the package maintainers directly? If R-help is the wrong place, please feel free to direct me to the correct one. I am on debian (testing) linux 64 with the binary R distribution from the

Esteemed R-forum subscribers, I'm having a tough time configuring contrasts for my 3-way ANOVA. In short: I don't know how to configure (all) my contrasts correctly in order to specify (all) my comparisons of interest. I succeeded getting my contrasts of interest set up for a simpler 2-way ANOVA based on the fairly intuitive logic of the design col.names. But i'm not able to

Hi Chakravarthy, [dont forget to Cc the list for useRs with the same Q.] If you're trying to reuduce the isze of your row or column labels, i think the following arguments of heatmap.2 {gplots} is what you want to adjust- 'cexCol' and 'cexRow'. Specifically on my question that you ask about, i found the BioC forum helpful:

Hi there ! I've got 7 Samples that may contain 29 differents kinds of material.... every line below corresponds to a differente kind of material, example: Sample 1, 2,3,5 and 6 has material 1 .... So I want to know how can I do a Venn Diagram with the data below .... ps ( it was generated by a csv, where every line is sep with (";")) Can someone helps me ? thanks csv file :

Esteemed UseRs, I've got many biggish data frames which need a lot subsetting, like in this example: # example eg <- data.frame(A = rnorm(10), B = rnorm(10), C = rnorm(10), D = rnorm(10)) egsub <- eg[eg$A < 0 & eg$B < 1 & eg$C > 0, ] egsub egsub2 <- eg[eg$A > 1 & eg$B > 0, ] egsub2 # To make this clearer than 1000s of lines of extractions with [] # I

Esteemed R users and developers, How does one 'programatically' list or call objects for use in a function? For example, i thought i could do something better than this: save(A.cwb, B.cwb, C.cwb, D.cwb, E.cwb, F.cwb, file="afile.RData") with something like these- prfxs <- c("A", "B", "C", "D", "E", "F") #**

Dear R Users, I employed the phyper() function to estimate the likelihood that the number of genes overlapping between 2 different lists of genes is due to chance. This appears to work appropriately. Now i want to try this with 3 lists of genes which phyper() does not appear to support. Some googling suggests i can utilize the Multivariate hypergeometric distribution to achieve this. eg.: