HI Jim I run it like this: Rscript --no-save Manhattan_plot.R
and just in case I added: stringsAsFactors=FALSE so the script looks like this: library(qqman) results_log <- read.table("logistic_results_M3.assoc.logistic.C", head=TRUE,stringsAsFactors=FALSE) jpeg("M3.assoc.logistic.jpeg") manhattan(results_log,chr="CHR",bp="BP",p="P",snp="SNP", main = "Manhattan plot:logistic") dev.off() this code does work with another data set, the jpeg() does work. I will try now with PNG On Wed, Jun 10, 2020 at 5:17 PM Jim Lemon <drjimle...@gmail.com> wrote: > > Hi Ana, > The problem may be that the JPEG device doesn't handle transparency. > Perhaps PNG? > > Jim > > On Thu, Jun 11, 2020 at 6:48 AM Ana Marija <sokovic.anamar...@gmail.com> > wrote: > > > > Hello, > > > > I have a data frame like this: > > > > > head(tmp1) > > CHR BP Pold Pnew > > 1 1 785989 0.9521 0.09278 > > 2 1 1130727 0.4750 0.19010 > > 3 1 1156131 0.5289 0.48520 > > 4 1 1158631 0.2554 0.18140 > > 5 1 1211292 0.2954 0.48590 > > 6 1 1478153 0.5542 0.68790 > > ... > > > > I did: > > tmp.tidy <- tmp1 %>% gather(key, value, -BP, -CHR) > > jpeg("over.jpeg") > > ggplot(tmp.tidy, aes(BP, value, color=key)) + geom_point() + > > facet_wrap(~CHR, nrow=1) > > dev.off() > > > > but I got this plot in attach which doesn't make sense. Can you please > > advise how to make this plot? > > > > thanks > > Ana > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.