thank you,
it worked properly.
On Thu, Jan 15, 2009 at 4:53 AM, Marc Schwartz <marc_schwa...@comcast.net>wrote:
> on 01/14/2009 03:32 PM John Lande wrote:
> > dear all,
> >
> > I want to plot a kaplan Meier plot with the following functions, but I
> fail
> > to produce the plot I want:
> >
> > library(survival)
> > tim <- (1:50)/6
> > ind <- runif(50)
> > ind[ind > 0.5] <- 1; ind[ind < 0.5] <- 0;
> > MS <- runif(50)
> > pred <- vector()
> > pred[MS < 0.3] <- 0; pred[MS >= 0.3] <- 1
> > df <- as.data.frame(cbind(MS, tim, pred, ind))
> > names(df) <- c("MS", "time", "pred", "class")
> > df$time[df$time > 6] <- 6
> > surv <- Surv(as.numeric(as.vector(df$time)),
> > as.numeric(as.vector(df$class)))
> > dfPval <- summary(coxph(Surv(as.numeric(as.vector(df$time)),
> > as.numeric(as.vector(df$class))) ~ pred, df))$sctest
> > par(mfrow = c(2,2))
> > plot(survfit(surv ~ df$pred), col=c("red","green"), ylab = "percentage of
> > survival", xlab = "survival years")
> > plot(survfit(surv ~ df$pred), col=c("red","green"), lwd = 8, ylab =
> > "percentage of survival", xlab = "survival years")
> > plot(survfit(surv ~ df$pred), col=c("red","green"), lwd = 8, ylab =
> > "percentage of survival", xlab = "survival years", cex = 2)
> >
> > I would like to increase the tickness of the censorship's pitch. as you
> can
> > see with cex = 2, I can elongate the arms of the censorship, but I cant
> find
> > how to increase the tickness of the pitch.
> >
> > how to do this?
>
> John,
>
> Is this what you want?
>
>
> par(mfrow = c(2, 1))
>
> # Normal plot
> plot(survfit(Surv(time, status) ~ x, data = aml))
>
>
> # Set par(lwd = 3) to increase the thickness of the censoring marks
> # Don't frame the plot region, as it uses par(lwd)
> par(lwd = 3)
> plot(survfit(Surv(time, status) ~ x, data = aml), frame = FALSE)
>
> # Reset par(lwd) to normal to frame the plot region
> par(lwd = 1)
> box()
>
>
> Note that given the way in which the plot code has been set up, using
> 'lwd' in the function call affects the survivorship function line and
> not the censoring marks. By setting par(lwd = 3) prior to the plot call,
> this will be used internally when the marks are plotted using points(),
> without affecting the other lines, save the plot region frame.
>
> Just so that you don't think that you missed something obvious, this was
> a little trial and error after reviewing the R code for
> survival:::plot.survfit to see how the arguments from the function call
> are passed to the internal plotting functions. Combined also with some
> knowledge of how the graphic pars are handled...
>
> HTH,
>
> Marc Schwartz
>
>
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