similar to: finding the plot limits generated by default

Dear R community, I need to plot the results of some simulations I did using QTL Cartographer. I am plotting LOD scores over three chromosomes. The three plot have to be one next to the other. The procedure I am using is: par(mfrow=c(1,3)) plot(x$x, x$y, ylim=c(0,35), type="l", col="blue", las=1, xaxs="i", yaxs="i", xlab="X Chromosome",

> chromosomes id refseq name length 1 0 NC_000001.9 Homo sapiens chromosome 1 247249719 2 1 NC_000002.10 Homo sapiens chromosome 2 242951149 3 2 NC_000003.10 Homo sapiens chromosome 3 199501827 4 3 NC_000004.10 Homo sapiens chromosome 4 191273063 5 4 NC_000005.8 Homo sapiens chromosome 5 180857866 6 5 NC_000006.10 Homo sapiens chromosome 6

Hello, I have a list with gene names, fold changes (=expression level) and chromosomes. Names fold change chromosome hz 1.5 2 If I plot fold change versus chromosome (or vice versa): plot (ch, fc) I see only the chromosomes with numbers but not those with letter (x and y). What can I do? A second question: How can I add a single line in that plot at a certain

Dear R-Helpers, I am not very experienced in using lattice and I am still in the learning stage I have a data set which looks like this: (I have deleted a few lines in order to save space) Chromosome marker Marker.Name Distance 1 1 1 PeMm261 0.0000 2 1 2 Xtxp8 10.1013 .. 20 1 20 EbMi148 210.3099 21 1 21 Xtxp25

Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, > chromosome <- c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) >barplot (chromosome, col="purple", xlab="Oryza sativa Chromosomes", border = NA, space =

Howdy, I have read that if you put a URL in the text of a plot being saved into pdf, the result is a functional hyperlink. I am interested in having text in a plot that is linked to a URL, but I would like the text to be something other than the URL. Is this possible? Thank you. - Fincher

Hi, I would like some extra information on the 'cgh' package in R. I noticed that there isn't much activity regarding this package on the R and BioC mailing list (I googled it). I started using this package and I have few questions: 1/ As I have a custom tiling like array @8um features resolution (affy), I have a lot of probes to work with. I'm assuming it is correct to

Hello, I have an R script that I use as a template to perform a task for multiple files (in this case, multiple chromosomes). What I would like to do is to utilize a simple loop to parse through each chromosome number so that I don't have to type the same code over and over again in the R console. I've tried using: for(i in 1:22){ etc.. } and replacing each chromosome number with

Howdy, I have written a small function to generate a simple plot and my colleague is having an error when attempting to run it. Essentially I loop through categories in a data frame and take the average value for each category The categories are in $V1, subset first then mean taken and concatenated to previous values using rbind(c("label",mean(data$V6)). The result is a two-column

Dear all. I need to draw a scatter plot of 23 chromosome copy numbers (y axes) against chromosome and physical location within each chromosome in one plot. The data matrix looks as below: chr location copy_num 1 118345 1.320118 1 3776202 1.133879 1 4798845 0.989997 1 5350951 1.100967 . more data here . . 2 118345 2.459119 2 157739 1.915919 2 1530065 1.924372 2

Dear R-listers, I want to reperfrom a poisson distribution test that presented in a recent-published biological research paper (Plant Physiology 2008, vol 148, pp. 1189-1200). That test is about the occurrence number of a kind of gene in separate chromosomes. For instance: The observed gene number in chromosome A is 36. The expected gene number in chromosome A is 30. Then, the authors got a

Howdy, I am trying to make a simple monochrome heatmap from 1 row of data. Essentially, I just want a long bar where black represents the max value in the data, white is the minimum, and all values in between are interpolated appropriately. I have tried using heatmap and heatmap.2, but both have issues. heatmap seems to be restricted to only drawing a square plot, and this data requires a

Hi there, First off, despite this being my first post here, I have scanned the R help forums a lot in the past few months to help with some questions, so a big thank you to the community as a whole for being so helpful! I'm somewhat of an R newbie, and have run up against a problem that I can't seem to solve. If anyone is able to help I would really appreciate it! I'm looking at a

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here:

I am attempting to sample 10 markers from each chr, with a maximum distance of 14, calculated by the location of the marker in each chromosome as loc[i+1] - loc[i]. I presume the easiest way to do this is with a while loop, so that the function keeps resampling when the max distains is greater than 14. Example code is below. I have gon as far as to select markers and calculate the distances, A

Hi, Am am plotting aggregated frequency data (extracted from an RDBMS) relating to DNA sequence features for each of the human chromosomes as described in the table chromosomes below (the frequency data is in a table 'hits' that has a value (or not) for each of a set of bins across each chromosome). I would like to mark the extent of the chromosome (according to the length value in

Hi, List, Sorry in advance if this turns out to be a stupid question -- I've been trying to work it out for awhile, and I don't have any new ideas -- I'm very new to R documentation/ LATEX. I am running "R CMD check " on a package that I am trying to write; the only warning is: * checking for missing documentation entries ... WARNING Undocumented data sets: Einter KG All

Dearl list, can anyone point me to a function or library that can create a graph similar to the one in the following powerpoint presentation? http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt (pages 36-37) In order to try to explain the graph, the way I see it in R terms is something like this: the "p-q" axis is a vector of positions (for example, seq(0,5000000,1)) the

Hi, Recently added to doc/NEWS.Rd: 'R CMD check' now gives a warning rather than a note if it finds inefficiently compressed datasets. With 'bzip2' and 'xz' compression having been available since R 2.10.0, there is no excuse for not using them. Why isn't a note enough for this? Generally speaking, warnings are for things that are dangerous, or unsafe,

Howdy, This should be simple, but I am finding that I can't find a simple solution. I have a plot to which I am manually adding the annotations to the y-axis with this command: axis(2, c(-4,-3,-2,-1,0,1,2,3,4,5,6,7),labels=c(-4,-3,-2,-1,0,1,2,3,4,5,6,7),cex.axis=8) The issue is that, apparently, R doesn't think that the -1 can fit, even though there is most certainly enough space.