Kaplan-Meier Survival plot – with at risk table, by sub groups

This is a follow on from the previous post, with updated code.

There was an argument ‘groups’ in the ggplot(…) line of the code that was working but is now no longer working with the updated version of R/ggplot2 (I don’t know the full ins and outs of this sorry). So code is fixed and available below.

Most up-to-date code available here: http://pastebin.com/FjkWnCWm

Code originally included in this post: http://pastebin.com/yRmuZtPG

24 thoughts on “Kaplan-Meier Survival plot – with at risk table, by sub groups”

Pingback: Kaplan-Meier Survival Plot – with at risk table « Matt's Stats n stuff

Hi, that’s looking much cleaner than the previous version.
Just trying to workout what your subs parameter is for?

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Mark Cowley on May 6, 2012 at 10:56 am said:

ah, never mind, I missed the 1st version of your function where you go over this at length.

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Hy…I still can’t get the code to work.
Thanks for any help

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nzcoops on May 6, 2012 at 11:14 pm said:

Antonio, I’d be happy to help when I have time. But you’ve given me absolutely nothing to go off… Error message? Are you using your data or just the example from this and my last post?

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- antonio on May 11, 2012 at 2:00 pm said:
  
  Hi I am using my data. I have recently updated R. I now have R 2.15.0 (2012-03-30) for Mac and when i run the code I get this error message:
  Error in ggkm(fit, timeby = 6, ystratalabs = c(“Calcium salts”, “Sevelamer”), :
  could not find function “rbind.fill”
  Thanks for al you can tell me.
  Antonio
- nzcoops on June 21, 2012 at 7:47 am said:
  
  Hi Antonio. Hmm, I can only assume that it’s saying that could there is a package missing. Can you try
  
  install.packages(“plyr”)
  
  And then re run?
- antonio on June 25, 2012 at 8:55 pm said:
  
  THANKS MATT…I DID RELOAD THE PLYR PAKAGE…RE-RUN THE FUNCTION BUT IT STILL DOESN’T WORK…:-(
  THANKS ANYWAY
  A
- nzcoops on June 26, 2012 at 4:21 am said:
  
  Okay. Well I can see from your strata labels that you are using it on your own data. It would be good if you could use the example I used in the post to see if that runs. Then we would know if it was the function on your system that isn’t working or just an anomaly between your data and the function.
- SA on July 13, 2012 at 6:28 pm said:
  
  Error “could not find function “rbind.fill”” can be fixed by adding following lines under “libraries” in ggkm function:
  
  # libraries #
  #############
  
  require(ggplot2)
  require(survival)
  require(gridExtra)
  require(reshape) #rbind.fill function is in this package.
  require(plyr) #additional dependency.
  
  ################

Hey,

Your function works fine in R 2.14.0 (2011-10-31) now. Unfortunately, it won’t print a p-value anymore, even if I set pval = TRUE

Also, you might consider using pastebin (http://pastebin.com/) to upload your code with, makes it a bit easier imo.

Thanks for the help!
Petra

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Petra on May 7, 2012 at 9:36 am said:

Also, below
###################################
# specifying plot parameteres etc #
###################################

you have a loose ‘p’ in your code

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- Petra on May 7, 2012 at 9:37 am said:
  
  (line 96)
nzcoops on June 21, 2012 at 7:44 am said:

Thanks Petra, have removed that p that hung around from testing. .

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- Petra on June 21, 2012 at 7:46 am said:
  
  Thanks :) Love your function, keep up the good work!! ^.^

Thanks Petra, have removed the stray p, hang over from fixing the error. The p-value side of it still works for me, however when doing the subgroups the p-value that is used isn’t appropriate, not sure when I’ll get to look at this. Have migrated to pastebin.

Cheers

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Mark Cowley on May 8, 2012 at 10:11 pm said:

how about a quick & dirty to avoid reporting wrong p-vals:
if( !is.null(subs) ) pval <- FALSE

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- nzcoops on June 21, 2012 at 7:42 am said:
  
  Thanks Mark, have added this in the latest version.

Hello Matt,

first of all, great job with your ggkm function. I was searching for a nice function to plot (good looking) survivor curves and your function just fits in.

I have a question about setting the ystratalabs when not given to the function.

if(is.null(ystratalabs)) ystratalabs <- as.character(levels(summary(sfit)$strata)[subs1])

In case on of the strata has no events, so just censored observations, it would not show up in "summary(sfit)". As a consequece your ystratalabs have the wrong length. I got an error when trying the function:

Error in `levels<-.factor`(`*tmp*`, value = "group=G2") :
number of levels differs

Maybe I did something wrong ? Is it possible to set "ystratalabs" to "names(sfit$strata)" or is this the wrong order ?

Best regards,
Stephan

P.S.: Here is a minimal example producing the error above:

surv.table <- data.frame(time=runif(40, min=0, max=12),
status=c(rep(0,20), sample(c(0,1), 20, replace=T)),
group=rep(c("G1", "G2"), each=20)
)
sfit <- survfit(Surv(time, status)~group, data=surv.table)
ggkm(sfit)

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nzcoops on June 21, 2012 at 7:42 am said:

Thanks for the post. Sorry for the delay, I didn’t get an email about this until a pingback came through, oddly.

I’ve amended the code down the line you mentioned just adding a sub command to strip out the ‘group=’ from the front. Give it a go. Appreciate a quick reproducible example too! Good luck.

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- Stephan Gade on July 17, 2012 at 1:13 pm said:
  
  Hello Matt,
  
  now I have to apologize for the late answer. I wasn’t around for some weeks. I tested your new code and it works. Thank you very much! Excellent work!
  
  Stephan