Hi John,
Brilliant solution and the best sort - when you finally solve your
problem by yourself.
Jim
On Thu, Oct 1, 2020 at 2:52 AM array chip <arrayprof...@yahoo.com> wrote:
>
> Hi Jim,
>
> I found out why clip() does not work with lines(survfit.object)!
>
> If you look at code of function survival:::lines.survfit, in th middle of the
> code:
>
> do.clip <- getOption("plot.survfit")
> if (!is.null(xx <- do.clip$plotclip))
> clip(xx[1], xx[2], xx[3], xx[4])
>
> This will reset the clipping to the defualt plot region!
>
> So I just comment out the last 2 lines of the above 3 lines, and created a
> customized lines2 function. Now it works!
>
> It's fun to learn clip().
>
> Thanks,
>
> John
>
>
> On Wednesday, September 30, 2020, 01:47:55 AM PDT, Jim Lemon
> <drjimle...@gmail.com> wrote:
>
>
> Hi John,
> Hmmm, this works:
>
> plot(1:10)
> xylim<-par("usr")
> clip(5,xylim[2],xylim[3],xylim[4])
> lines(10:1)
>
> so I suspect that there is a "lines" method that resets the clipping
> region out of sight. Fortunately Mark Schwartz provided a way to get
> your plot so I will give the wall against which I have been banging my
> head a break.
>
> Jim
>
> On Wed, Sep 30, 2020 at 1:57 PM array chip <arrayprof...@yahoo.com> wrote:
> >
> > Jim,
> >
> > I tried a few things, I found that clip() works if I just do some regular
> > graphing tasks. But as long as I run lines(fit) with "fit" object is a
> > survfit object, this would reset to default plot region. See the ovarian
> > example below:
> >
> > library(survival)
> > ovarian1<-ovarian
> > ovarian1$fustat[ovarian$futime>450]<-0
> > ovarian1$futime[ovarian$futime>450]<-450
> > ovarian2<-subset(ovarian,futime>450)
> >
> > fit1 <- survfit(Surv(futime, fustat) ~ rx, data = ovarian1)
> > fit2 <- survfit(Surv(futime, fustat) ~ rx, data = ovarian2)
> >
> > plot(fit1, xlim=c(0,1200), col = 1:2)
> > abline(v=450)
> > xylim<-par("usr")
> > points(-1,-1)
> > clip(450,xylim[2],xylim[3],xylim[4])
> > abline(h=0.5,col=2) ### YES, clipping() works!
> >
> > lines(fit2, col = 3:4,lty=2) ### clipping does not work! reset to default
> > plot region
> > abline(h=0.4,col=2) ### NO, clipping() does not work!
> >
> > So disappointed with this, otherwise this would be such a simple method to
> > do what I want.
> >
> > Thanks,
> >
> > John
> >
> > On Tuesday, September 29, 2020, 07:58:53 PM PDT, Jim Lemon
> > <drjimle...@gmail.com> wrote:
> >
> > Hi John,
> > I should have remembered this. For some reason, the clip() function
> > doesn't operate until you have issued a graphics command. Try:
> >
> > points(-1,-1)
> >
> > before calling lines()
> >
> > Jim
> >
> > On Wed, Sep 30, 2020 at 12:26 PM array chip <arrayprof...@yahoo.com> wrote:
> > >
> > > Hi Jim,
> > >
> > > I tried the clip() function below, surprisingly it did not work! I read
> > > the R help file and feel your script should work. To have a workable
> > > example, I used the ovarian dataset in the survival package as an example:
> > >
> > > ovarian1<-ovarian
> > > ovarian1$fustat[ovarian$futime>450]<-0
> > > ovarian1$futime[ovarian$futime>450]<-450
> > >
> > > ovarian2<-subset(ovarian,futime>450)
> > >
> > > fit1 <- survfit(Surv(futime, fustat) ~ rx, data = ovarian1)
> > > fit2 <- survfit(Surv(futime, fustat) ~ rx, data = ovarian2)
> > >
> > > plot(fit1, xlim=c(0,1200), col = 1:2)
> > > abline(v=450)
> > > xylim<-par("usr")
> > > clip(450,xylim[2],xylim[3],xylim[4])
> > > lines(fit2, col = 3:4,lty=2)
> > >
> > > I can still see that the extra horizontal line on the top.
> > >
> > > Can you or anyone have any suggestion what went wrong?
> > >
> > > Thanks,
> > >
> > > John
> > >
> > >
> > > On Tuesday, September 29, 2020, 01:35:48 AM PDT, Jim Lemon
> > > <drjimle...@gmail.com> wrote:
> > >
> > >
> > >
> > >
> > >
> > > Hi John,
> > > Perhaps the most direct way would be:
> > >
> > > plot(fit1, col=1:2)
> > > xylim<-par("usr")
> > > clip(4,xylim[2],xylim[3],xylim[4])
> > > lines(fit2,col=1:2)
> > >
> > > Remember that the new clipping rectangle will persist until you or
> > > something else resets it.
> > >
> > > Jim
> > >
> > > On Tue, Sep 29, 2020 at 10:34 AM array chip via R-help
> > > <r-help@r-project.org> wrote:
> > > >
> > > > Hello,
> > > >
> > > > Can anyone suggest a simple way to generate a Kaplan-Meier plot with 2
> > > > survfit objects, just like this one:
> > > >
> > > > https://drive.google.com/file/d/1fEcpdIdE2xYtA6LBQN9ck3JkL6-goabX/view?usp=sharing
> > > >
> > > > Suppose I have 2 survfit objects: fit1 is for the curve on the left
> > > > (survtime has been truncated to the cutoff line: year 5), fit2 is for
> > > > the curve on the right (minimum survival time is at the cutoff line:
> > > > year 5), but if I do the following:
> > > >
> > > > plot(fit1, col=1:2)
> > > > lines(fit2,col=1:2)
> > > >
> > > > Then I will have an horizontal line on the top that connect from 0 to 4
> > > > years, which I do not want that to be drawn (see blue arrow below):
> > > >
> > > > https://drive.google.com/file/d/178mQGlhnaOg9PA-oE-W_W5CtrGD03ljH/view?usp=sharing
> > > >
> > > > Can anyone have a strategy to make this kind of plot happen?
> > > >
> > > > Thanks,
> > > >
> > > > John
> > >
> > > >
> > > > ______________________________________________
> > > > R-help@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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