align graph and table with same x-axis in ggplot2

[Misha]

How can I align the survival curve with the table in the following
kaplan meier function so that the x-axis is corresponding between the
table and the graph ? As it is now the interval between the "ticks" is
less in the table. Any ideas?

//M

Cudos to the learnr website for the table plotting method:-)

example using ggkm (albeit a poor dataset) in the end of the code.

function ggkm:

ggkm<-
function(time,event,stratum="-1",tit="",xscale=round(seq(0,max(time),by=max(time)/
10),0)) {
lev<-levels(factor(stratum))
w2<-lev[1]!="-1"

if (w2) {stratum<-as.factor(stratum)}

m2s<-Surv(time,as.numeric(event))
if (w2) {fit <- survfit(m2s~stratum)}
else fit<-survfit(m2s~-1)

w<-fit$time

k<-fit$surv

o<-length(levels(stratum))

strata<-c(rep(names(fit$strata[1:o]),fit$strata[1:o]))
lev2<-levels(as.factor(strata))
upper<-fit$upper
lower<-fit$lower
if (w2) {f<-data.frame(w,k,strata,upper,lower)}
else f<-data.frame(w,k,upper,lower)
if (w2) {r<-ggplot (f,aes(x=w,y=k,fill=strata,group=strata))
+geom_line(aes(color=strata))+scale_fill_brewer(f
$strata,palette="Set1")+scale_color_brewer(f$strata,palette="Set1")}
else r<-ggplot(f,aes(x=w,y=k))+geom_line()
r<-r
+geom_ribbon(aes(ymin=lower,ymax=upper),alpha=0.3)+opts(title=tit)
r<-r
+opts(panel.grid.minor=theme_blank(),panel.grid.major=theme_blank(),panel.background=theme_blank(),axis.line=theme_segment())
r<-r+opts(legend.position=c(0.8,0.8))
#r<-r+opts(legend.title="")
if (w2) {
r<-r
+scale_fill_brewer("",palette="Set1",breaks=lev2,labels=lev)
+scale_color_brewer("",palette="Set1",breaks=lev2,labels=lev)
}
r<-r+geom_hline(yintercept=0.5,linetype=2)
r+expand_limits(x = 0, y = 0)+scale_x_continuous("Observation time
(months)",expand = c(0,
0),breaks=xscale,labels=xscale,limits=c(min(xscale),max(xscale)))
+scale_y_continuous("Probability of overall survival
(proportion)",expand = c(0,0))->r


##number at risk table
u<-llply(names(fit$strata),function(x) rep(x,fit$strata[x]))
p<-ldply(u,function(x) data.frame(x))
fit2<-data.frame(p,fit$n.risk,fit$surv,fit$time,fit$n.event)
q<-dlply(fit2,.(x),function(g) data.frame(g$fit.n.risk,g$fit.surv,g
$fit.time,g$fit.n.event))
e<-ldply(q,function(y){
o<-ldply(xscale,function(x) y[min(which((x-y$g.fit.time<0))),1])
oo<-cbind(o,xscale)
})
melt(e,id=c("xscale","x"))->e2
e2$strata<-as.factor(e2$x)
cast(subset(e2,e2$variable!="x.time"),strata~xscale,identity)->e3
#e3[["strata"]]<-names(e3[["strata"]])
dg<-
ggplot(e2,aes(x=xscale,y=strata,color=strata,label=format(factor(value),nsmall=1)))
+geom_text(size=2.5)+theme_bw()
+scale_color_brewer(e2$strata,palette="Set1")

#levels(e2$strata)<-lev
dg<-dg+scale_y_discrete(limits=e2$strata)+expand_limits(x=0,y=0)
dg<-dg
+opts(panel.grid.minor=theme_blank(),panel.grid.major=theme_blank(),panel.background=theme_blank(),axis.line=theme_blank())
dg<-dg
+opts(panel.border=theme_blank(),axis.text.x=theme_blank(),axis.text.y=theme_blank(),axis.ticks=theme_blank())
#dg<-dg
+opts(panel.border=theme_blank(),axis.text.x=theme_blank(),axis.ticks=theme_blank())

dg<-dg+opts(plot.margin = unit(c(-0.5,1, 0, 0.5), "lines")) +
xlab(NULL) + ylab(NULL)+labs(colour="")
dg<-dg+opts(legend.position="none")
##Same page
Layout <- grid.layout(nrow = 2, ncol = 1, heights =
unit(c(2,0.25), c("null", "null")))

grid.show.layout(Layout)

vplayout <- function(...) {
grid.newpage()
pushViewport(viewport(layout = Layout))
}
subplot <- function(x, y) viewport(layout.pos.row =
x,layout.pos.col = y)

mmplot <- function(a, b) {
vplayout()
print(a, vp = subplot(1, 1))
print(b, vp = subplot(2, 1))
}
t<-mmplot(r, dg)

return(t)
}


library(survival)
require(ggplot2)
data(leukemia)
with(leukemia,ggkm(time,status,x,tit="Leukemia"))

[Brian Diggs]

I didn't go though your code in detail, but it seems you are trying to
align the axes of two different plots. Check out the align.plots
function from ggExtra on google code/R-forge:

http://code.google.com/p/ggextra/

https://r-forge.r-project.org/projects/ggplot-add-ons/

Also check out previous discussion about aligning plots:

http://groups.google.com/group/ggplot2/browse_thread/thread/855def93677ef722/

http://groups.google.com/group/ggplot2/browse_thread/thread/1b859d6b4b441c90/

--
Brian S. Diggs, PhD
Senior Research Associate, Department of Surgery
Oregon Health & Science University