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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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
On Tue, Feb 11, 2020 at 3:46 PM Ana Marija <sokovic.anamarija at
gmail.com> wrote:>
> 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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Hi Ana, Okay, it's the lattice package. Try this: panel.abline(v=-4) panel.text(-3.9,0.35,"*") As I don't have your data I can't provide a complete example. Jim On Wed, Feb 12, 2020 at 8:50 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:> > 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 > > On Tue, Feb 11, 2020 at 3:46 PM Ana Marija <sokovic.anamarija at gmail.com> wrote: > > > > 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.