Adding ggsurvfit version of kaplan.meier

DESCRIPTION

@@ -16,4 +16,5 @@ Imports:
     survival,
     stats
 Suggests: 
-    ggplot2
+    ggplot2,
+    ggsurvfit

R/km.R

@@ -31,3 +31,107 @@ kaplan.meier<-function(x,var,comment=''){
     graphics::legend("top",legend=lLab,col=cols,lty=c(1,1),horiz=FALSE, bty='n')
     p
 }
+
+set.from.list<-function(var,default,...){
+   z<-list(...)
+   if (var %in% base::names(z)) result<-base::unlist(z[[var]])
+   else result=default
+   result
+}
+
+#' Plot a Kaplan-Meier curve with ggsurvfit
+#'
+#'@param x data frame containing followup and censored column
+#'@param var name of variable to stratify by
+#'@param ... other parameters:
+#' * varName name of variable for title (NOT GIVEN)
+#' * comment additional text to print on plot (empty string)
+#' * reorder whether to change order of categorical variable labels in legend (FALSE)
+#' * unit unit for time axis
+#' * my.legend.title title to set to legend (varName)
+#' * my.title title for the plot (Kaplan-Meier plot by varName)
+#' * my.labels labels for cases
+#' * draw.axis draw title and axis (FALSE)
+#' * my.n number of classes (2)
+
+kaplan.meier.plot.gg<-function(x,var,...){
+   if (!requireNamespace('ggsurvfit',quiet=TRUE)){
+      print('ggsurvfit not available. Use rNIX::kaplan.meier function')
+      return(NULL)
+   }
+
+ 
+	#x should have followup and censored columns	
+	surv.obj<-survival::Surv(x$.followup,x$.censored)
+   m=base::max(x$.followup)
+
+	f<-stats::as.formula(paste('surv.obj',var,sep='~'))
+   #need survfit2
+	s1<-ggsurvfit::survfit2(f,data=x)
+       
+   varName=set.from.list('varName','NOT GIVEN',...)
+  	tit=base::sprintf('Kaplan-Meier plot by %s',varName)
+        
+   comment=set.from.list('comment','',...)
+   my.labels=set.from.list('my.labels',c(),...)
+   reorder=set.from.list('reorder',FALSE,...)
+   unit=set.from.list('unit','day',...)
+   my.legend.title=set.from.list('my.legend.title','NONE',...)
+   draw.axis=set.from.list('draw.axis',FALSE,...)
+   my.title=set.from.list('my.title',tit,...)
+   my.n=set.from.list('my.n',2,...)
+      
+   
+   
+   base::print(base::sprintf('my.n=%f',my.n))
+   
+   xlab=base::sprintf('Time (%ss)',unit)
+   ylab='Overall survival probability'
+   if (my.n==4)
+    	cols=base::c('dodgerblue2', 'orchid2','orange','green')
+   else	
+      cols=base::c('dodgerblue2', 'orchid2')
+       
+   nc=base::length(cols)
+   base::print(base::sprintf('nc=%d',nc))
+       
+   labs <- base::gsub("^.*=","",base::names(s1$strata))  ## legend labels
+   if (base::length(my.labels)==0){
+    	my.labels <- labs
+   }
+    
+   nl=base::length(labs)
+   nl1=base::length(my.labels)
+   base::print(base::sprintf('nl=%d nl1=%d',nl,nl1))
+       
+    
+   if (my.legend.title=='NONE'){
+       my.legend.title=varName
+   }
+ 	if (reorder){
+       perm=base::c(2,1)
+       cols=cols[base::order(perm)]
+       labs=labs[base::order(perm)]
+       my.labels=my.labels[base::order(perm)]
+       
+    }    
+    q<-ggsurvfit::ggsurvfit(s1,lwd=1.0,censor=TRUE,censor.shape='+',censor.size=10)+
+         ggplot2::ylim(0,1)+
+   	   ggsurvfit::add_legend_title(my.legend.title)+
+   		ggsurvfit::add_pvalue("annotation", size = 5)+
+        #add_pvalue("caption", size = 5)+
+         ggsurvfit::add_confidence_interval()+
+   		#add_risktable()+
+    	   ggplot2::scale_color_manual(values=cols,breaks = labs,labels=my.labels) +
+  		   ggplot2::scale_fill_manual(values=cols, breaks = labs,labels=my.labels) +
+   		ggplot2::labs(x=NULL, y=NULL)
+    if (draw.axis){
+        q<-q+ggplot2::ggtitle(my.title)+ggplot2::xlab(xlab)+ggplot2::ylab(ylab)
+    }
+   		
+    
+    q
+    
+   		
+                         
+}

man/kaplan.meier.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/km.R
+\name{kaplan.meier}
+\alias{kaplan.meier}
+\title{Create a KM plot}
+\usage{
+kaplan.meier(x, var, comment = "")
+}
+\arguments{
+\item{x}{a data frame that contains followup and censored columns}
+
+\item{var}{a categorical variable to split the data to sub-curves}
+
+\item{comment}{An additional piece of text to write in the curve}
+}
+\value{
+p probability that curves split by var differ significantly
+}
+\description{
+Create a KM plot
+}

man/kaplan.meier.plot.gg.Rd

@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/km.R
+\name{kaplan.meier.plot.gg}
+\alias{kaplan.meier.plot.gg}
+\title{Plot a Kaplan-Meier curve with ggsurvfit}
+\usage{
+kaplan.meier.plot.gg(x, var, ...)
+}
+\arguments{
+\item{x}{data frame containing followup and censored column}
+
+\item{var}{name of variable to stratify by}
+
+\item{...}{other parameters:
+\itemize{
+\item varName name of variable for title (NOT GIVEN)
+\item comment additional text to print on plot (empty string)
+\item reorder whether to change order of categorical variable labels in legend (FALSE)
+\item unit unit for time axis
+\item my.legend.title title to set to legend (varName)
+\item my.title title for the plot (Kaplan-Meier plot by varName)
+\item my.labels labels for cases
+\item draw.axis draw title and axis (FALSE)
+\item my.n number of classes (2)
+}}
+}
+\description{
+Plot a Kaplan-Meier curve with ggsurvfit
+}