similar to: problem tick marker and text

Hello all, I am trying to make a genome association plot for p-values related to SNPs and was fortunate to find that R contains a package that produces Manhattan plots which is what's preferred for my current project. The function mhtplot() is found in the 'gap' package which I installed in R 2.11.1 on Windows. I thought I'd test out the function first with the examples they

Hello All: I was wondering why many plot options are not working with mhtplot. I could not find much info about this function on the web too. Any comments, any detailed manual ... Thanks, MJK [[alternative HTML version deleted]]

Hello, I am trying to create a simple Manhattan plot for a small list of 200 SNPs spread out in the genome in different genes. I have tried different functions (using ggplot2 and a function created by Stephen Turner, mhtplot etc.)-none of them work smoothly. Does anyone have a simple way to create the plot (not for all 22 chromosomes)- with the x axis showing the genes name and not the

Hi Readers, I have a question. I have a large dataset and want to throw away columns that have the same value in the column itself and I want to know which column this was. For example > x<-data.frame(id=c(1,2,3), snp1=c("A","G", "G"),snp2=c("G","G","G"),snp3=c("G","G","A"))

Hi all, A simple question which I don???t seem to be able to solve: I want to make a data.frame of 360 rows and 94228 column with only zero???s without having to type all these zero???s ;-) What is the easiest method? Thanks, Naomi Disclaimer: De informatie opgenomen in dit bericht (en bijlagen) kan vertrouwelijk zijn en is uitsluitend bestemd voor

R folks, I am trying to create a mhtplot plot that will alter the point size via the plot point value. The size of the point should change via a set criteria such as: if point value <10^-6 size 3x else if 10^-3> point value >10^-6 size 2x else point value >10^-3 size is x I consider myself an R newbie, and I am assuming that I could do this via some sort of function to change

Hi all, I want to make extra columns in my datafile where the id of every groupmember is mentioned in separate columns. To explain it better see the example: id<-c(1,2,3,4,5,6,7,8,9,10,11,12) group<-c(1,1,1,1,2,2,3,3,3,3,3,3) a<-as.data.frame(cbind(id,group)) a id group 1 1 1 2 2 1 3 3 1 4 4 1 5 5

Hi, I have a large dataset on which I would like to do the following: x<-data.frame(id=c(1,2,3), snp1=c("AA","GG", "AG"),snp2=c("GG","AG","GG"),snp3=c("GG","AG","AA")) > x id snp1 snp2 snp3 1 1 AA GG GG 2 2 GG AG AG 3 3 AG GG AA And then

Hi, I am trying to split multiple columns. One column works just fine, but I want to do it for multiple columns??? Example > a ID V2 V3 V4 V5 V6 V7 V8 V9 V10 1 PBBA0644 -- GG AA -- AA -- AA GG GG 2 PBBA1010 -- GG AA -- AA -- AA GG GG 3 0127ATPR -- GG AA -- AA -- AA GG GG 4 0128EHAB -- GG AA -- AG -- AA AG GG 5 PBBA0829 -- GG AA -- AA -- AA GG AG

Hi, I need a custom axis function for a plot, but it seems that current.panel.limits() sometimes returns NaN limits for the plot, which it much harder to calculate anything sensible. An illustration: Given this axis function: vs.axis <- function(...){ xlim <- current.panel.limits()$xlim ylim <- current.panel.limits()$ylim # Debug code print(list(ylim=ylim,xlim=xlim))

Have made a stacked area plot, but now want to manipulate the x axis: make in even increments (50) in order to suppress the tick marks (forming solid bar under plot). However, the plot functions do not seem to work, and I cannot find documentation for use of xat in stackpoly. This is a time series of data covering 579 years, and has been successfully converted from zoo to matrix. Data plotting

I would like to make the print format of the axis value labels appear as ``nn%'' instead of just the numbers. Is there a way to do this? Also, the x axis value labels on my horizontal barplot are rotated 90 degrees (perpendicular to the axis) no matter what I do. I tried las=1 but that didn't work. Is this doable? Thanks. $platform [1] "i686-pc-linux-gnu" $arch [1]

Hi, I have a data set like this: Mutant Rep Time OD 02H02 1 0 0.029 02H02 2 0 0.029 02H02 3 0 0.023 02H02 1 8 0.655 02H02 2 8 0.615 02H02 3 8 0.557 02H02 1 12 1.776 02H02 2 12 1.859 02H02 3 12 1.668 02H02 1 16 3.379 02H02 2 16 3.726 02H02 3 16 3.367 306 1 0 0.033 306 2

Dear all, I am fairly new to package Plotrix and I would like to ask you, if any of you could help me with following. a) I don't know how to set up border line width in the Stackpoly function (seems that lwd from par doesn't work, or at least not in the way I have written) b) I don't know, how to rotate the x axis labels (I used srt=45, but same problem as before). c) Could anyone

I have the following graphic where I drop unused factors in the x axis, however I cannot get the first point on the second panel. It seems shifted. Any ideas? The example is below: data <- data.frame( Room=as.factor(c(132,132,132,132,132,132,132,132,132,196,196)),

Hi, I'm having trouble plotting populations as separate colors and points in the 3d scatterplot package. I have a column with 4 different population names and 3 columns with my data. I want to plot each population with a different color and pch. In addition, I want to use the type="h" in my plotting so that I can see the points clearly in my graph( for publication purposes).

Dear all, How can I make an index plot with lattice, that is plotting a vector simply against its particular index in the vector, i.e. something similar to y <- rnorm(10) plot(y) I don't want to specify the x's manually, as this could become cumbersome when having multiple panels. I tried something like library(lattice) mp <- function(x, y, ...) { x <- 1:length(y)

Hello list, I read in a txt file using <B<-read.table(file="data.snp",header=TRUE,row.names=NULL) by specifying the row.names=NULL so that the rows are numbered. Below is an example after how the table looks like using <B[1:10,1:3] SNP Chromosome PhysicalPosition 1 SNP_A-1909444 1 7924293 2 SNP_A-2237149 1 8173763

Is there anyway to label axes in 3D plots with mathematical expressions? In the code below, I want to replace "delta_yrsed" with what "\Delta \widehat{yrsed}" represents in TeX, but the [xyz]lab parameters of title3d appear to only accept character strings. require("rgl") fn.delta.yrsed <- function(dist, delta.dist,

I would like to create a 3d scatterplot that is interactive in the sense that I can spin it on its axes to better visualize some PCA results I have. What are the options in R? I've looked at RGL and perhaps it will suffice but it wasn't apparent from the documentation I found. Any demo scripts available for a package that will work? Mark -- Mark W. Kimpel MD ** Neuroinformatics **