R help - Nov 2012 - 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"
          )




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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

>  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

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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:maziar.mohaddes at gmail.com] 
Sent: Tuesday, November 06, 2012 11:11 AM
To: r-help at r-project.org
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"
          )




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http://r.789695.n4.nabble.com/Survplot-Y-axis-in-percent-tp4648572.html
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