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.
