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
cpoiw@rt m@iii@g oii chemo@org@uk
2020-Jun-11 14:26 UTC
[R] How to stack two Stack manhattan plots?
On 2020-06-11 14:54, Ana Marija wrote:> Hello, > > I expected it to look like this: > https://imgur.com/a/pj40c >Ah - so all on the one plot? - so you don't want a facet. It puts two plots side by side (or 22)> where x-axis would be CHR, there is 22 of them >> unique(tmp.tidy$CHR) > [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 >You have 22 plots all appearing side by size as part of the facet I think you want color=CHR - but I don't know what your current color setting is doing.> I also have two phenotypes (keys) which I would like to compare >> unique(tmp.tidy$key) > [1] "Pold" "Pnew" >So did you want to Facet those?
yes all in one plot. So I want key (and therefore color)to be "Pold" and "Pnew" as those I am comparing per CHR so I used facet_wrap(~CHR) to create a graph per chromosome (on x-axis) On the end x-axis would have two strikes of Pold and Pnew (different colors) per one chromosome, and CHR would go from 1 to 22 On Thu, Jun 11, 2020 at 9:26 AM <cpolwart at chemo.org.uk> wrote:> > On 2020-06-11 14:54, Ana Marija wrote: > > Hello, > > > > I expected it to look like this: > > https://imgur.com/a/pj40c > > > > Ah - so all on the one plot? - so you don't want a facet. It puts two > plots side by side (or 22) > > > where x-axis would be CHR, there is 22 of them > >> unique(tmp.tidy$CHR) > > [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 > > > > You have 22 plots all appearing side by size as part of the facet > > I think you want color=CHR - but I don't know what your current color > setting is doing. > > > I also have two phenotypes (keys) which I would like to compare > >> unique(tmp.tidy$key) > > [1] "Pold" "Pnew" > > > > So did you want to Facet those?