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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2020-06-10 at 3.34.47 PM.png Type: image/png Size: 311087 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20200610/59234ecb/attachment.png>
?dput We cannot tell how the columns are being stored in memory from your head() output. On June 10, 2020 1:36:11 PM PDT, Ana Marija <sokovic.anamarija at 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-- Sent from my phone. Please excuse my brevity.
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.anamarija at 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 at 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.
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 <drjimlemon at 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.anamarija at
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 at 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.
On Wed, 10 Jun 2020 15:36:11 -0500 Ana Marija <sokovic.anamarija at 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 > AnaIf you would, the str() output might help people understand what is happening, and also how many records you're looking at. The head() output is a bit thin on information. There are various manhattan plot packages for R including a specialized package for ggplot2. JWDougherty
Hello, I expected it to look like this: https://imgur.com/a/pj40c where x-axis would be CHR, there is 22 of them> unique(tmp.tidy$CHR)[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 I also have two phenotypes (keys) which I would like to compare> unique(tmp.tidy$key)[1] "Pold" "Pnew"> dim(tmp.tidy)[1] 2600184 4 I would like the x-axis to be separated by CHR> sapply(tmp.tidy,class)CHR BP key value "integer" "integer" "character" "numeric"> str(tmp.tidy)'data.frame': 2600184 obs. of 4 variables: $ CHR : int 1 1 1 1 1 1 1 1 1 1 ... $ BP : int 785989 1130727 1156131 1158631 1211292 1478153 1500941 1506035 1510801 1721479 ... $ key : chr "Pold" "Pold" "Pold" "Pold" ... $ value: num 0.952 0.475 0.529 0.255 0.295 ... Unfortunately qqman doesn't do this kind of overlay of two plots On Wed, Jun 10, 2020 at 11:24 PM John <jwd at surewest.net> wrote:> > On Wed, 10 Jun 2020 15:36:11 -0500 > Ana Marija <sokovic.anamarija at 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 > > If you would, the str() output might help people understand what is > happening, and also how many records you're looking at. The head() > output is a bit thin on information. There are various manhattan plot > packages for R including a specialized package for ggplot2. > > JWDougherty