# Survplot, Y-axis in percent

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## Survplot, Y-axis in percent

 Hi I am a new fan of R after getting mad with the graphical functional in SPSS. I have been able to create a nice looking Kaplan Meyer graph using Survplot function. However I have difficulties in turning the y axis to percent instead of the default 0-1 scale. Further I have tried the function yaxt="n" without any results. Any help in this matter will be appreciated. The code is posted below: par(mfrow=c(1,1)) fit <- survfit(Surv(revreg\$Tcuprev , revreg\$Rcup_n_j_n)~revreg\$RAceGrp_1Maz) fit survplot (fit, col=c("gray1","gray40"), lty=1, lwd = 1, col.fill=c("gray50","gray80"),           mark.time= T,  conf="bands" , conf.int=.95, add=F ,           xlim=c(0, 20) , time.inc = 4,           ylim=c(0.5, 1),           xlab="Years Postoperative" , ylab="Cumulative Survival Probability" ,           label.curves=F , abbrev.label=F ,           yaxt="n"           ) Maziar Mohaddes, MD Gothenburg, Sweden
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## Re: Survplot, Y-axis in percent

 On Nov 6, 2012, at 8:10 AM, maziar.mohaddes wrote: > Hi > > I am a new fan of R after getting mad with the graphical functional in SPSS. > I have been able to create a nice looking Kaplan Meyer graph using Survplot > function. > However I have difficulties in turning the y axis to percent instead of the > default 0-1 scale. > Further I have tried the function yaxt="n" without any results. Any help in > this matter will be appreciated. > The code is posted below: > > par(mfrow=c(1,1)) > fit <- survfit(Surv(revreg\$Tcuprev , revreg\$Rcup_n_j_n)~revreg\$RAceGrp_1Maz) Probably better in the future to supply a data argument and then you formula only needs the column names. > fit > survplot (fit, col=c("gray1","gray40"), lty=1, lwd = 1, > col.fill=c("gray50","gray80"), >          mark.time= T,  conf="bands" , conf.int=.95, add=F , >          xlim=c(0, 20) , time.inc = 4, >          ylim=c(0.5, 1), >          xlab="Years Postoperative" , ylab="Cumulative Survival > Probability" , >          label.curves=F , abbrev.label=F , >          yaxt="n" >          ) As far as I can see, survplot.survfit (from package rms) is written with base graphics, so you need to suppress the default axis call with yaxt=FALSE, and replace it with your desired values using axis(2, at=..., labels=...). No testing in the absence of data. > > View this message in context: http://r.789695.n4.nabble.com/Survplot-Y-axis-in-percent-tp4648572.html> Sent from the R help mailing list archive at Nabble.com. You should also realize that Nabble is not Rhelp. -- David Winsemius, MD Alameda, CA, USA ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: Survplot, Y-axis in percent

 >  As far as I can see, survplot.survfit (from package rms) is written with base graphics, so you need to suppress the >  default axis call with yaxt=FALSE, and replace it with your desired values using axis(2, at=..., labels=...). Thanks alot for your response. Unfortunately yaxt function does not seem to be supported  in survplot (rms package). > You should also realize that Nabble is not Rhelp. Obviously My post has been malplaced, could u please guide me in where to place to post? Thanks in advance -- Maziar Mohaddes, MD Gothenburg, Sweden ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. Maziar Mohaddes, MD Gothenburg, Sweden
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## Re: Survplot, Y-axis in percent

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## Re: Survplot, Y-axis in percent

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## Re: Survplot, Y-axis in percent

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## Re: Survplot, Y-axis in percent

 In reply to this post by maziar.mohaddes It doesn't look like 'survplot' allows you to control the yaxis formatting in that way.  You can edit the function survplot.survfit directly if you really need to: fix(survplot.survfit).  The relevant line to change is (I believe) mgp.axis(2, at = pretty(ylim)) to mgp.axis(2, at = pretty(ylim), labels= 100*pretty(ylim)).  However, if you are new to R this could cause you more trouble than you want. Alternatively, you can use 'plot' with the yaxt="n" option. e.g., mod <- survfit(Surv(time,status)~ph.ecog, data=lung) plot(mod, yaxt="n", col=1:4, ylab="Survival Percent", xlab="Days", main="Lung Cancer Data\nEffect of ph.ecog on Survival") axis(2, at=seq(0,1,0.2), labels=paste(seq(0,100,20), "%", sep=""), las=1) But that doesn't have all the other stuff you appear to want (e.g., shaded confidence bands). Good luck, Chris -----Original Message----- From: maziar.mohaddes [mailto:[hidden email]] Sent: Tuesday, November 06, 2012 11:11 AM To: [hidden email] Subject: [R] Survplot, Y-axis in percent Hi I am a new fan of R after getting mad with the graphical functional in SPSS. I have been able to create a nice looking Kaplan Meyer graph using Survplot function. However I have difficulties in turning the y axis to percent instead of the default 0-1 scale. Further I have tried the function yaxt="n" without any results. Any help in this matter will be appreciated. The code is posted below: par(mfrow=c(1,1)) fit <- survfit(Surv(revreg\$Tcuprev , revreg\$Rcup_n_j_n)~revreg\$RAceGrp_1Maz) fit survplot (fit, col=c("gray1","gray40"), lty=1, lwd = 1, col.fill=c("gray50","gray80"),           mark.time= T,  conf="bands" , conf.int=.95, add=F ,           xlim=c(0, 20) , time.inc = 4,           ylim=c(0.5, 1),           xlab="Years Postoperative" , ylab="Cumulative Survival Probability" ,           label.curves=F , abbrev.label=F ,           yaxt="n"           ) -- View this message in context: http://r.789695.n4.nabble.com/Survplot-Y-axis-in-percent-tp4648572.htmlSent from the R help mailing list archive at Nabble.com. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.