similar to: alternate tick labels and tick marks with lattice xyplot

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

> 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

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

My question is twofold. Part 1: My data looks like this: (example set, real data has 2*10^6 rows) binary<-c(1,1,1,0,0,0,1,1,1,0,0) Chromosome<-c(1,1,1,1,1,1,2,2,2,2,2) start<-c(12,17,18,20,25,36,12,15,16,17,19) Table<-cbind(Chromosome,start,binary) Chromosome start binary [1,] 1 12 1 [2,] 1 17 1 [3,] 1 18 1 [4,] 1

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 =

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

Hello, I'm writing some genetic simulations in R where I would like to place genes along a chromosome proportional to the density of markers in a given region. For example, a chromosome can be presented as a list of marker locations: Chr1<-c(0, 6.5, 17.5, 26.2, 30.5, 36.4, 44.8, 45.7, 47.8, 48.7, 49.2, 50.9, 52.9, 54.5, 56.5, 58.9, 61.2, 64.1) Where the numbers refer to the locations of

Dear all, Probably a very basic question but I need some help. I have a data frame (made by read.table from a text file) of microarray data, of which the first column is a factor and the rest of the columns are numeric. The factor column contains chromosome names, so values 1 through 22 plus X, Y and XY. The numeric columns contain positions or intensity measurements. What I need to do is

Hi,     I want to use segChrom() method in tilingArray package. For that I need to create a probeAnno object. I could not find much much info by ?probeAnno. I need help in creating  probeAnno object. Snap shot of the file(.txt): chr1 2500014 2500038 + 0.232689943122845 chr1 2500039 2500063 + 2.60502410304227 chr1 2500062 2500086 + 0.0756595313279895 chr1 2500080 2500104 + 0.78574617788405 chr1

Hi, is there any package/function in Bioconductor that can do this: if given the chromosome positions of a fragment, find out all genes within, and with the information about which strand is the sense strand. And vice versa. Thanks a lot. ----- Appreciate your time & attention! -- View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html

Dear colleagues, I've just come across a problem with the following command which is a part of the "metaOverview.R" code file provided as an monography- accompanying file at http://www.bioconductor.org/docs/mogr/metadata: ################################## R> hasChr <- eapply(GOTERM, function(x) + x[grep("chromosome", Term(x))]) Error in

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:

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

I have the following xyplot figure: http://img577.imageshack.us/img577/686/filesizeresults12000000.png The data are organized in a matrix file as follows: Type Elements Chromosome Time bedGz 12000000 chr1 14.240 bedGz 12000000 chr2 7.949 bedGz 12000000 chr3 5.103 bedGz 12000000 chr4 5.290 bedGz 12000000 chr5 5.161 ... The x-axis labels in the Chromosome column are ordered

Hi all, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency.

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",

Hi,? I have two big data set.? data _1 :? > dim(data_1) [1] 15820 5 > head(data_1) ? ?Chromosome ?????Start????????End????????Feature GroupA_3 1: ? ? ? ????????chr1 521369 ?750000 ????chr1-0001 ? ?????0.170 2: ? ? ? ????????chr1 750001 ?800000 ????chr1-0002 ? ????-0.086 3: ? ? ? ????????chr1 800001 ?850000 ????chr1-0003 ? ?????0.006 4: ? ? ? ????????chr1 850001 ?900000 ????chr1-0004 ?

Hi, This is another question relating to my 2 factor figure. densityplot(~End-Begin | Type * Chromosome, data=Mon, layout=c(5,12), xlab="Element Length",type="percent", col="grey60", strip=strip.custom(style=3, bg="grey90", par.strip.text=list(cex=0.5))) I would like to flip the plot so those at the bottom are at the top and so on. I have tried using a

Dear list, I have a data frame (238304 rows and 6 columns). I want the data frame sorted by two columns in ascending order. I am showing the first 5 rows of the data frame > clones.info[1:5,1:6] USER_CLONE_ID CHROMOSOME Expr1002 KB_POSITION Allele_A WELL_ID 1 SNP_A-1855402 17 41419603 41419603 C rs17572851 2 SNP_A-4249904 17 41420045 41420045 A rs17572893 3 SNP_A-2174835 18 41407760