[R] 2 KM curves on the same plot
array chip
@rr@ypro|||e @end|ng |rom y@hoo@com
Wed Sep 30 05:45:38 CEST 2020
Hi Jim,
I tried points(-1,-1) before lines() and before clip(), but either way, it still shows everything, :-(
It's interesting that the examples with hist() provided by the R help of clip function works nicely.
I also tried a simple linear regression plots below, clip() works, too.
dat<-data.frame(x=1:10,y=1:10)
fit<-lm(y~x,dat)
plot(1:10)
abline(fit)
xylim<-par("usr")
clip(6,xylim[2],xylim[3],xylim[4])
abline(fit,col=2) ## yes, it only shows the fit line from 6 to the right
lines(c(2,8),c(5,5)) ## yes, it only shows the line from 6 to the right
So it's puzzling that only when using lines() with a survfit() object (ovarian example below), somehow clip() doesn't work
John
On Tuesday, September 29, 2020, 07:58:53 PM PDT, Jim Lemon <drjimlemon using 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 <arrayprofile using 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 <drjimlemon using 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 using 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 using 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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