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 at 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
Please supply sample data in dput() format See ?dput. You might find these links helpful. http://adv-r.had.co.nz/Reproducibility.html http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example On Tue, 11 Feb 2020 at 15:07, Ana Marija <sokovic.anamarija at gmail.com> wrote:> 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 at 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 > > ______________________________________________ > R-help at 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. >-- John Kane Kingston ON Canada [[alternative HTML version deleted]]
Hi Ana,
Your image didn't make it through (as usual). Try PNG or PDF format.
Assumptions
1) You want to plot two lines using the _paired_ values of inter- and
intra-individual variance.
2) The cases are in the same order in your data
3) You want to identify the two lines
4) You want to place text with some p-value between the lines
This is really (and suspiciously) simple. Here's a start:
tot<-read.table(text="dat type
-3.962 inter.individual.variance
-4.301 inter.individual.variance
-1.690 inter.individual.variance
-0.375 inter.individual.variance
1.816 inter.individual.variance
0.138 inter.individual.variance
-4.09 intra.individual.variance
-4.64 intra.individual.variance
-5.57 intra.individual.variance
-2.96 intra.individual.variance
-4.43 intra.individual.variance
-3.60 intra.individual.variance",
header=TRUE)
# get the numeric values of the factor 'type'
tot$ntype<-as.numeric(tot$type)
plot(tot$dat[tot$ntype==1],type="l",col="green",ylim=range(tot$dat))
lines(tot$dat[tot$ntype==2],col="blue")
text(5,-1.5,"p = 0.005")
legend(1,1,c("Inter-individual variance","Intra-individual
variance"),
lty=1,col=c("green","blue"))
Jim
On Wed, Feb 12, 2020 at 7:07 AM Ana Marija <sokovic.anamarija at
gmail.com> wrote:>
> 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 at
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
>
> ______________________________________________
> R-help at 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.
Hi Jim
I tried your code and it didn't show me density curves.
However I was able to do teh plot myself via:
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 it is attached. The only thing I need to do is to make a line in
between peaks of the curves and put the star above that line. Not a p
value but just a star symbol.
Please advise,
Thanks
Ana
On Tue, Feb 11, 2020 at 3:23 PM Jim Lemon <drjimlemon at gmail.com>
wrote:>
> Hi Ana,
> Your image didn't make it through (as usual). Try PNG or PDF format.
>
> Assumptions
> 1) You want to plot two lines using the _paired_ values of inter- and
> intra-individual variance.
> 2) The cases are in the same order in your data
> 3) You want to identify the two lines
> 4) You want to place text with some p-value between the lines
>
> This is really (and suspiciously) simple. Here's a start:
>
> tot<-read.table(text="dat type
> -3.962 inter.individual.variance
> -4.301 inter.individual.variance
> -1.690 inter.individual.variance
> -0.375 inter.individual.variance
> 1.816 inter.individual.variance
> 0.138 inter.individual.variance
> -4.09 intra.individual.variance
> -4.64 intra.individual.variance
> -5.57 intra.individual.variance
> -2.96 intra.individual.variance
> -4.43 intra.individual.variance
> -3.60 intra.individual.variance",
> header=TRUE)
> # get the numeric values of the factor 'type'
> tot$ntype<-as.numeric(tot$type)
>
plot(tot$dat[tot$ntype==1],type="l",col="green",ylim=range(tot$dat))
> lines(tot$dat[tot$ntype==2],col="blue")
> text(5,-1.5,"p = 0.005")
> legend(1,1,c("Inter-individual variance","Intra-individual
variance"),
> lty=1,col=c("green","blue"))
>
> Jim
>
> On Wed, Feb 12, 2020 at 7:07 AM Ana Marija <sokovic.anamarija at
gmail.com> wrote:
> >
> > 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 at
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
> >
> > ______________________________________________
> > R-help at 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.
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