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 <drjimlemon at
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 at 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
at 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 at 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 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 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 <arrayprofile at 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 <drjimlemon
at 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 at
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 at 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 at 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 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.
> >
Thank you Jim for helping! Yes, I will try Mark's method.
John
On Wednesday, September 30, 2020, 01:47:55 AM PDT, Jim Lemon <drjimlemon at
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 <arrayprofile at 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 <drjimlemon
at 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 at
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 at 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 at 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 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 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$plotclip))?
? ? ? ? clip(xx[1], xx[2], xx[3], xx[4])
This will reset the clipping to the defualt plot region!
So I just comment out the last 2 lines of the above 3 lines, and created a
customized lines2 function. Now it works!
It's fun to learn clip().
Thanks,
John
On Wednesday, September 30, 2020, 01:47:55 AM PDT, Jim Lemon <drjimlemon at
gmail.com> wrote:
Hi John,
Hmmm, this works:
plot(1:10)
xylim<-par("usr")
clip(5,xylim[2],xylim[3],xylim[4])
lines(10:1)
so I suspect that there is a "lines" method that resets the clipping
region out of sight. Fortunately Mark Schwartz provided a way to get
your plot so I will give the wall against which I have been banging my
head a break.
Jim
On Wed, Sep 30, 2020 at 1:57 PM array chip <arrayprofile at yahoo.com>
wrote:>
> Jim,
>
> I tried a few things, I found that clip() works if I just do some regular
graphing tasks. But as long as I run lines(fit) with "fit" object is a
survfit object, this would reset to default plot region. See the ovarian example
below:
>
> library(survival)
> ovarian1<-ovarian
> ovarian1$fustat[ovarian$futime>450]<-0
> ovarian1$futime[ovarian$futime>450]<-450
> ovarian2<-subset(ovarian,futime>450)
>
> fit1 <- survfit(Surv(futime, fustat) ~ rx, data = ovarian1)
> fit2 <- survfit(Surv(futime, fustat) ~ rx, data = ovarian2)
>
> plot(fit1, xlim=c(0,1200), col = 1:2)
> abline(v=450)
> xylim<-par("usr")
> points(-1,-1)
> clip(450,xylim[2],xylim[3],xylim[4])
> abline(h=0.5,col=2)? ? ? ### YES, clipping() works!
>
> lines(fit2, col = 3:4,lty=2)? ### clipping does not work! reset to default
plot region
> abline(h=0.4,col=2)? ? ? ### NO, clipping() does not work!
>
> So disappointed with this, otherwise this would be such a simple method to
do what I want.
>
> Thanks,
>
> John
>
> On Tuesday, September 29, 2020, 07:58:53 PM PDT, Jim Lemon <drjimlemon
at gmail.com> wrote:
>
> Hi John,
> I should have remembered this. For some reason, the clip() function
> doesn't operate until you have issued a graphics command. Try:
>
> points(-1,-1)
>
> before calling lines()
>
> Jim
>
> On Wed, Sep 30, 2020 at 12:26 PM array chip <arrayprofile at
yahoo.com> wrote:
> >
> > Hi Jim,
> >
> > I tried the clip() function below, surprisingly it did not work! I
read the R help file and feel your script should work. To have a workable
example, I used the ovarian dataset in the survival package as an example:
> >
> > ovarian1<-ovarian
> > ovarian1$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 at 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 at 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 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.
> >