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.-------------- next part -------------- A non-text attachment was scrubbed... Name: newp.png Type: image/png Size: 141973 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20200211/bd030a1f/attachment.png>