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
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______________________________________________
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.
