I could make legend via this: qq(fdr2_sorted$FDR.q.val2, main = "RG_All", pch = 16, col=fdr1_sorted$group, cex = 0.8, las = 1) legend('topleft', legend = c('up-regulated', 'down-regulated'), fill = c('red', 'blue'),bty="o")
but this gives me squares in legend. How do I write this code in order to have circles in the legend? On Thu, Mar 12, 2020 at 11:04 AM Ana Marija <sokovic.anamar...@gmail.com> wrote: > > Also how would I add legend to this plot? > > I searched qqman pages and there is no mention of that > > qq(fdr2_sorted$FDR.q.val2, main = "RG_All", pch = 16, > col=fdr1_sorted$group, cex = 0.8, las = 1) > > On Thu, Mar 12, 2020 at 9:30 AM Ana Marija <sokovic.anamar...@gmail.com> > wrote: > > > > Hi Michael, > > > > can you please send me a line of code showing how it would be done. > > > > Thanks > > Ana > > > > On Thu, Mar 12, 2020 at 9:16 AM Michael Dewey <li...@dewey.myzen.co.uk> > > wrote: > > > > > > Dear Ana > > > > > > You can specify the first three parameters to text() as vectors so it is > > > all done in one call. That may or may not answer your question. > > > > > > Michael > > > > > > On 12/03/2020 14:08, Ana Marija wrote: > > > > HI David, > > > > > > > > thank you for getting back to me. > > > > > > > > Is there is a way for qq() to pick up text label names on its own or I > > > > have to specify each one manually? > > > > like in this example: > > > > text( 2, 6, "arbitrary") > > > > > > > > this is dput for > > > > > > > >> a=head(fdr2_sorted) > > > >> dput(a) > > > > structure(list(NAME = c("GO_DNA_PACKAGING_COMPLEX", > > > > "GO_PROTEIN_DNA_COMPLEX", > > > > "GO_RESPONSE_TO_TYPE_I_INTERFERON", "GO_RESPONSE_TO_INTERFERON_GAMMA", > > > > "GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA", "GO_GRANULOCYTE_MIGRATION" > > > > ), `GS<br> follow link to MSigDB` = c("GO_DNA_PACKAGING_COMPLEX", > > > > "GO_PROTEIN_DNA_COMPLEX", "GO_RESPONSE_TO_TYPE_I_INTERFERON", > > > > "GO_RESPONSE_TO_INTERFERON_GAMMA", > > > > "GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA", > > > > "GO_GRANULOCYTE_MIGRATION"), `GS DETAILS` = c("Details ...", > > > > "Details ...", "Details ...", "Details ...", "Details ...", "Details > > > > ..." > > > > ), SIZE = c(77L, 132L, 52L, 101L, 85L, 43L), ES = c(0.6757226, > > > > 0.59581786, -0.7521569, -0.63704145, -0.6571892, -0.7332099), > > > > NES = c(2.466745, 2.3465202, -2.5331483, -2.4204733, -2.4021535, > > > > -2.3989832), `NOM p-val` = c(0, 0, 0, 0, 0, 0), `FDR q-val` = c(0, > > > > 0, 0, 0, 0, 0), `FWER p-val` = c(0, 0, 0, 0, 0, 0), `RANK AT MAX` > > > > = c(1111L, > > > > 1516L, 1427L, 1819L, 1216L, 491L), `LEADING EDGE` = c("tags=43%, > > > > list=10%, signal=47%", > > > > "tags=39%, list=13%, signal=45%", "tags=54%, list=12%, signal=61%", > > > > "tags=45%, list=16%, signal=52%", "tags=38%, list=11%, signal=42%", > > > > "tags=28%, list=4%, signal=29%"), V12 = c(NA, NA, NA, NA, > > > > NA, NA), FDR.q.val2 = c(1e-10, 1e-10, 1e-10, 1e-10, 1e-10, > > > > 1e-10)), class = c("data.table", "data.frame"), row.names = c(NA, > > > > -6L), .internal.selfref = <pointer: 0x10400bae0>) > > > > > > > >> b=head(fdr1_sorted) > > > >> dput(b) > > > > structure(list(NAME = c("GO_DNA_PACKAGING_COMPLEX", > > > > "GO_PROTEIN_DNA_COMPLEX", > > > > "GO_RESPONSE_TO_TYPE_I_INTERFERON", "GO_RESPONSE_TO_INTERFERON_GAMMA", > > > > "GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA", "GO_GRANULOCYTE_MIGRATION" > > > > ), `GS<br> follow link to MSigDB` = c("GO_DNA_PACKAGING_COMPLEX", > > > > "GO_PROTEIN_DNA_COMPLEX", "GO_RESPONSE_TO_TYPE_I_INTERFERON", > > > > "GO_RESPONSE_TO_INTERFERON_GAMMA", > > > > "GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA", > > > > "GO_GRANULOCYTE_MIGRATION"), `GS DETAILS` = c("Details ...", > > > > "Details ...", "Details ...", "Details ...", "Details ...", "Details > > > > ..." > > > > ), SIZE = c(77L, 132L, 52L, 101L, 85L, 43L), ES = c(0.6757226, > > > > 0.59581786, -0.7521569, -0.63704145, -0.6571892, -0.7332099), > > > > NES = c(2.466745, 2.3465202, -2.5331483, -2.4204733, -2.4021535, > > > > -2.3989832), `NOM p-val` = c(0, 0, 0, 0, 0, 0), `FDR q-val` = c(0, > > > > 0, 0, 0, 0, 0), `FWER p-val` = c(0, 0, 0, 0, 0, 0), `RANK AT MAX` > > > > = c(1111L, > > > > 1516L, 1427L, 1819L, 1216L, 491L), `LEADING EDGE` = c("tags=43%, > > > > list=10%, signal=47%", > > > > "tags=39%, list=13%, signal=45%", "tags=54%, list=12%, signal=61%", > > > > "tags=45%, list=16%, signal=52%", "tags=38%, list=11%, signal=42%", > > > > "tags=28%, list=4%, signal=29%"), V12 = c(NA, NA, NA, NA, > > > > NA, NA), group = c(2, 2, 4, 4, 4, 4), FDR.q.val2 = c(1e-10, > > > > 1e-10, 1e-10, 1e-10, 1e-10, 1e-10)), class = c("data.table", > > > > "data.frame"), row.names = c(NA, -6L), .internal.selfref = <pointer: > > > > 0x10400bae0>) > > > > > > > > library(qqman) > > > > qq(fdr2_sorted$FDR.q.val2, main = "RG_All", pch = 16, > > > > col=fdr1_sorted$group, cex = 0.8, las = 1) > > > > > > > > Please advise > > > > > > > > On Wed, Mar 11, 2020 at 11:21 PM David Winsemius > > > > <dwinsem...@comcast.net> wrote: > > > >> > > > >> > > > >> On 3/10/20 9:51 PM, Ana Marija wrote: > > > >>> Hello, > > > >>> > > > >>> I am making QQ plot via: > > > >>> > > > >>> library(ggman) > > > >>> qq(fdr2_sorted$FDR.q.val2, main = "RG_All", pch = 17, > > > >>> col=fdr1_sorted$group, cex = 1, las = 1) > > > >> > > > >> > > > >> I think you may be confusing the audience. There is no qq function in > > > >> the ggman package. There is however a qq function in the qqman package. > > > >> > > > >> > > > >> Running the example in help page for qqman::qq and looking at the code > > > >> suggests this is a base plot function, so the text function will allow > > > >> you to put any particular string within the plot area: > > > >> > > > >> library(qqman) > > > >> > > > >> qq(gwasResults$P) > > > >> text( 2, 6, "arbitrary") # puts text "arbitrary" at postion (x=2, y=6) > > > >> > > > >>> > > > >>> data frames used look like this: > > > >>> > > > >>>> head(fdr1_sorted) > > > >> > > > >> You should use `dput` to post reproducible data examples. > > > >> > > > >> HTH; > > > >> > > > >> David. > > > >> > > > >>> NAME GS<br> > > > >>> follow > > > >>> link to MSigDB GS DETAILS SIZE ES NES NOM p-val > > > >>> 1: GO_DNA_PACKAGING_COMPLEX > > > >>> GO_DNA_PACKAGING_COMPLEX Details ... 77 0.6757226 2.466745 > > > >>> 0 > > > >>> 2: GO_PROTEIN_DNA_COMPLEX > > > >>> GO_PROTEIN_DNA_COMPLEX Details ... 132 0.5958179 2.346520 0 > > > >>> 3: GO_RESPONSE_TO_TYPE_I_INTERFERON > > > >>> GO_RESPONSE_TO_TYPE_I_INTERFERON Details ... 52 -0.7521569 -2.533148 > > > >>> 0 > > > >>> 4: GO_RESPONSE_TO_INTERFERON_GAMMA > > > >>> GO_RESPONSE_TO_INTERFERON_GAMMA Details ... 101 -0.6370415 -2.420473 > > > >>> 0 > > > >>> 5: GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA > > > >>> GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA Details ... 85 -0.6571892 > > > >>> -2.402153 0 > > > >>> 6: GO_GRANULOCYTE_MIGRATION > > > >>> GO_GRANULOCYTE_MIGRATION Details ... 43 -0.7332099 -2.398983 > > > >>> 0 > > > >>> FDR q-val FWER p-val RANK AT MAX LEADING EDGE > > > >>> V12 > > > >>> group FDR.q.val2 > > > >>> 1: 0 0 1111 tags=43%, list=10%, signal=47% NA > > > >>> 2 1e-10 > > > >>> 2: 0 0 1516 tags=39%, list=13%, signal=45% NA > > > >>> 2 1e-10 > > > >>> 3: 0 0 1427 tags=54%, list=12%, signal=61% NA > > > >>> 4 1e-10 > > > >>> 4: 0 0 1819 tags=45%, list=16%, signal=52% NA > > > >>> 4 1e-10 > > > >>> 5: 0 0 1216 tags=38%, list=11%, signal=42% NA > > > >>> 4 1e-10 > > > >>> 6: 0 0 491 tags=28%, list=4%, signal=29% NA > > > >>> 4 1e-10 > > > >>> > > > >>>> head(fdr2_sorted) > > > >>> NAME GS<br> > > > >>> follow > > > >>> link to MSigDB GS DETAILS SIZE ES NES NOM p-val > > > >>> 1: GO_DNA_PACKAGING_COMPLEX > > > >>> GO_DNA_PACKAGING_COMPLEX Details ... 77 0.6757226 2.466745 > > > >>> 0 > > > >>> 2: GO_PROTEIN_DNA_COMPLEX > > > >>> GO_PROTEIN_DNA_COMPLEX Details ... 132 0.5958179 2.346520 0 > > > >>> 3: GO_RESPONSE_TO_TYPE_I_INTERFERON > > > >>> GO_RESPONSE_TO_TYPE_I_INTERFERON Details ... 52 -0.7521569 -2.533148 > > > >>> 0 > > > >>> 4: GO_RESPONSE_TO_INTERFERON_GAMMA > > > >>> GO_RESPONSE_TO_INTERFERON_GAMMA Details ... 101 -0.6370415 -2.420473 > > > >>> 0 > > > >>> 5: GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA > > > >>> GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA Details ... 85 -0.6571892 > > > >>> -2.402153 0 > > > >>> 6: GO_GRANULOCYTE_MIGRATION > > > >>> GO_GRANULOCYTE_MIGRATION Details ... 43 -0.7332099 -2.398983 > > > >>> 0 > > > >>> FDR q-val FWER p-val RANK AT MAX LEADING EDGE > > > >>> V12 > > > >>> FDR.q.val2 > > > >>> 1: 0 0 1111 tags=43%, list=10%, signal=47% NA > > > >>> 1e-10 > > > >>> 2: 0 0 1516 tags=39%, list=13%, signal=45% NA > > > >>> 1e-10 > > > >>> 3: 0 0 1427 tags=54%, list=12%, signal=61% NA > > > >>> 1e-10 > > > >>> 4: 0 0 1819 tags=45%, list=16%, signal=52% NA > > > >>> 1e-10 > > > >>> 5: 0 0 1216 tags=38%, list=11%, signal=42% NA > > > >>> 1e-10 > > > >>> 6: 0 0 491 tags=28%, list=4%, signal=29% NA > > > >>> 1e-10 > > > >>> > > > >>> and I would like to get the plot like the one in attach. > > > >>> > > > >>> Please advise, > > > >>> 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. > > > > > > > > > > -- > > > Michael > > > http://www.dewey.myzen.co.uk/home.html ______________________________________________ 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.