search for: mhtplot

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 give in the documentation: # foo example test <- matrix(c(1,1,4,1,1,6,1,10,3,2,1,5,2,2,6,2,4,8),byrow=TRUE,6) mhtplot(test) mhtplot(test,logsca...

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]]

...markers and normally the labels are printed at the place where the tick marker is placed. I don???t want to move the tick marker (it gives the switch between one chromosome and the next) but I just want to put the chromosome number in between the two tick markers. This example from mhtplot has the chromosome number at the place of the tickmarker. How can I change this to ???in between???? Thanks!, Naomi # fake example with Affy500k data affy <-c(40220, 41400, 33801, 32334, 32056, 31470, 25835, 27457, 22864, 28501, 26273, 24954, 19188, 15721, 14356, 15309,...

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 chromosomal location. Thanks a lot, Einat [[alternative HTML version deleted]]

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...

To whom it may concern: My name is Jillian Weinfeld. I am currently and undergraduate student at New York University and working at Mount Sinai School of Medicine doing research with epilepsy patients. At the moment I am creating a manhattan plot with my data set. After reading many forums and such, I have appropriately plotted my data, however, I wanted to see how I can change the colors of the