[R] how do I add text lables on QQ plot

[David Winsemius]

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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