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sachsmc / ggkm

Compute and display Kaplan-Meier Curves with ggplot2
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Using a Stepped version of ribbon for the confidence bands ? #6

Closed smouksassi closed 8 years ago

smouksassi commented 8 years ago

Hi thanks for the nice and only real extension to ggplot to include a KM "stat". I have an issue which is probably related to nousing a stepped ribbon for the confidence intervals. This result in sometimes truncating the ribbon see below the ecog 2 curve while the ecog 3 curve is not shown at all it only appears in the legend : Compare:

library(survival)
library(rms)
lung$SurvObj <- with(lung, Surv(time, status == 2))
km.by.ecog <- npsurv(SurvObj ~ ph.ecog , data = lung)
survplot(fit  = km.by.ecog, conf = c("bands"))

rms survplot output rmsplot

ggplot(lung, aes(time = time, status = ifelse(
          status == 2,1,0),col=as.factor(ph.ecog ),fill=as.factor(ph.ecog ))) +
 geom_km(fill="transparent")+ stat_km(geom="ribbon",alpha=0.1,color="black")+ # this to make the legend include the fill
          geom_kmticks()

geom_km /stat_km output (ecog 2 ribbon truncated, ecog 3 not shown): stat_kmplot

A potential solution is to use code from but it is only a stat we might need to add a "step_ribbon" geom: https://groups.google.com/forum/?fromgroups=#!topic/ggplot2/9cFWHaH1CPs

sachsmc commented 8 years ago

Thanks for pointing this out, I will work on adding it into the package.

smouksassi commented 8 years ago 
                                                                                  ‎ggalt has it already maybe just import it?https://github.com/hrbrmstr/ggaltThank you for the followup.Samer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         From: Michael SachsSent: Tuesday, August 2, 2016 08:42To: sachsmc/ggkmReply To: sachsmc/ggkmCc: Samer Mouksassi; AuthorSubject: Re: [sachsmc/ggkm] Using a Stepped version of ribbon for the confidence bands ? (#6)Thanks for pointing this out, I will work on adding it into the package.

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sachsmc commented 8 years ago

Try it out now using the master branch. install_github("sachsmc/ggkm") The grey line that appears is for the single case where ph.ecog is NA.

fix