[R] how to create density plot in R with p value

[Ana Marija]

so I transformed my data from the previous email to look like this:

> head(tot)
     dat                      type
1 -3.962 inter.individual.variance
2 -4.301 inter.individual.variance
3 -1.690 inter.individual.variance
4 -0.375 inter.individual.variance
5  1.816 inter.individual.variance
6  0.138 inter.individual.variance
> tail(tot)
        dat                      type
31177 -4.09 intra.individual.variance
31178 -4.64 intra.individual.variance
31179 -5.57 intra.individual.variance
31180 -2.96 intra.individual.variance
31181 -4.43 intra.individual.variance
31182 -3.60 intra.individual.variance

then I can make plot using this:

densityplot(~dat,data=tot,
       groups=type,
       par.settings = list(superpose.line = list(col = c("blue","red"))),
       xlab="log2 (variance)",
       plot.points=FALSE,
       auto.key=TRUE)

and calculate my p value with t test, say it is 0.005

But how to add that p value in between distribution of the curves?

Thanks
Ana

On Tue, Feb 11, 2020 at 12:54 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> Hi,
>
> I have data like this:
>
> > head(a)
>                    X   geneID inter.individual.variance
> intra.individual.variance F.value  p.value     CV
> 1 3iUZ.47hLFki49VR4o   MLLT10                    0.0642
>    0.01395    4.60 1.00e-05 0.0222
> 2 fEn1QlU0MCVe9GeR64 C1orf123                    0.0507
>    0.00671    7.57 1.00e-08 0.0172
> 3 ud_tTlU5LtB478JxIk    FSD1L                    0.3100
>    0.02682   11.56 1.00e-11 0.0639
> 4 3KV3OJIIRuJ5KJ6VkI  TXNDC11                    0.7710
>    0.02813   27.41 9.99e-19 0.0688
> 5 o_rupcEAKnQqnoh6ec   CYB5R2                    3.5209
>    0.03391  103.83 9.99e-31 0.1357
> 6 Nk_t6ULcQ7VDNChBRU     GBP1                    1.1005
>    0.09522   11.56 9.98e-12 0.0773
>
> I would like to create density plot, like the attached between
> "inter.individual.variance" and "intra.individual.variance" and have p
> value between those two curves.
>
> Please advise,
> Ana