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结果运行后报错，求帮助。
报错trackback如下：
Error in parse(text = x, keep.source = FALSE) :
<text>:2:0: unexpected end of input
1: srv~
^
7.
parse(text = x, keep.source = FALSE)
6.
eval(parse(text = x, keep.source = FALSE)[[1L]])
5.
formula(eval(parse(text = x, keep.source = FALSE)[[1L]]))
4.
formula.character(object, env = baseenv())
3.
formula(object, env = baseenv())
2.
as.formula(paste("srv~", marker))
1.
ggsrv(time = "RFS", event = "resultR", data = data)
Error in parse(text = x, keep.source = FALSE) :
<text>:2:0: unexpected end of input
1: srv~
^
7.
parse(text = x, keep.source = FALSE)
6.
eval(parse(text = x, keep.source = FALSE)[[1L]])
5.
formula(eval(parse(text = x, keep.source = FALSE)[[1L]]))
4.
formula.character(object, env = baseenv())
3.
formula(object, env = baseenv())
2.
as.formula(paste("srv~", marker))
1.
ggsrv(time = "RFS", event = "resultR", data = data)
原代码如下：
- ggsrv<-function(
- time="os",
- event="death",
- event.marker=1,
- marker="",
- tabletitle="",
- xlab="Months since surgery",
- ylab="Overall Survival rate",
- ystratalabs=c("High", "Low"),
- pval=TRUE,
- n.risk=FALSE,
- timeby=2,
- xmax=16,
- fun="survival",
- data = dat,
- conf.int=FALSE,
- returns = F,
- ...)
- {
- #Load the related packages
- require(ggplot2)
- require(survival)
- require(gridExtra)
- require(grid)
- require(plyr)
- require(cowplot)
- #create survival fit and data
- srv <- Surv(data[,time], data[,event]==event.marker)
- form <- as.formula(paste("srv~",marker))
- sfit=survfit(form,data = data)
- sdiff=survdiff(form,data = data)
-
- if(is.null(ystratalabs)) {
- ystratalabs <- as.character(levels(summary(sfit)$strata))
- }
-
- m <- max(nchar(ystratalabs))
- # if(xmax<=max(sdata$time)){
- # xlims=c(0, round(xmax/timeby, digits=0)*timeby)
- # }else{
- # xlims=c(0, round((max(sdata$time))/timeby, digits=0)*timeby)
- # }
-
- times <- seq(0, xmax, by = timeby)
-
- sdata <- data.frame(time = sfit$time,
- n.risk = sfit$n.risk,
- n.event = sfit$n.event,
- surv = sfit$surv,
- strata = summary(sfit, censored = T)$strata,
- upper = sfit$upper,
- lower = sfit$lower,
- n.censor = sfit$n.censor)
-
- levels(sdata$strata) <- ystratalabs
-
- zeros <- data.frame(time = 0,
- surv = 1,
- strata = factor(ystratalabs, levels=levels( sdata$strata)),
- upper = 1,
- lower = 1,
- n.censor=0)
-
- sdata <- rbind.fill(zeros, sdata)
-
-
- d <- length(levels(sdata$strata))
-
- dat.cens <- subset(sdata, n.censor != 0)
-
- if (fun=="event"){
-
- p <- ggplot(sdata, aes(x = time, y = 1-surv,group = strata, colour = strata)) +
- geom_step(size = 1) +
- scale_x_continuous(xlab, breaks = times, limits = c(0, max(times)), expand = c(0, 0)) +
- scale_y_continuous(ylab, breaks=seq(0,1,by=0.2), limits=c(0,1),
- labels=c(as.character(seq(0,0.8,by=0.2)),"1.0"),expand = c(0, 0)) +
- theme_classic() +
- theme(axis.title.x = element_text(vjust = 0.5)) +
- theme(panel.grid.minor = element_blank()) +
- theme(legend.position = c(ifelse(m < 10, .28, .15), ifelse(d < 4, .75, .95))) +
- theme(legend.key = element_rect(colour = NA)) +
- ggtitle(tabletitle)+
- geom_point(data = subset(sdata, n.censor != 0), aes(x = time, y = 1-surv), shape = 3)
-
- }else{
- p <- ggplot(sdata, aes(x = time, y = surv,group = strata, colour = strata)) +
- geom_step(size = 1) +
- scale_x_continuous(xlab, breaks = times, limits = c(0, max(times)), expand = c(0, 0)) +
- scale_y_continuous(ylab, breaks=seq(0,1,by=0.2), limits=c(0,1),
- labels=c(as.character(seq(0,0.8,by=0.2)),"1.0"),expand = c(0, 0)) +
- theme_classic() +
- theme(axis.title.x = element_text(vjust = 0.5)) +
- theme(panel.grid.minor = element_blank()) +
- theme(legend.position = c(ifelse(m < 10, .28, .15), ifelse(d < 4, .35, .45))) +
- theme(legend.key = element_rect(colour = NA)) +
- ggtitle(tabletitle)+
- geom_point(data = subset(sdata, n.censor != 0), aes(x = time, y = surv), shape = 3)
-
- }
-
- #Add P value to plot
-
- if(pval) {
- sdiff <- survdiff(eval(sfit$call$formula), data = eval(sfit$call$data))
- pval <- pchisq(sdiff$chisq, length(sdiff$n)-1, lower.tail = FALSE)
- pvaltxt <- ifelse(pval < 0.0001, "p < 0.0001", paste("p =", signif(pval, 3)))
- p <- p + annotate("text", x = 0.75 * max(times), y = 0.15, label = pvaltxt)
- }
-
-
- if(n.risk) {
- ## Create table graphic to include at-risk numbers
- risk.data <- data.frame(strata = summary(sfit, times = times, extend = TRUE)$strata,
- time = as.numeric(as.factor(summary(sfit, times = times, extend = TRUE)$time)),
- n.risk = summary(sfit, times = times, extend = TRUE)$n.risk)
-
- data.table <- ggplot(risk.data, aes(x = time, y = strata,
- label = format(n.risk, nsmall = 0))) +
- #, color = strata)) +
- geom_text(size=4) +
- scale_y_discrete(breaks = as.character(levels(risk.data$strata)),
- labels = ystratalabs) +
-
- scale_x_discrete(expand = c(0, 0))+
- theme(
- panel.grid.major = element_blank(),
- legend.position = "none",
- plot.background = element_blank(),
- panel.grid.major = element_blank(),
- panel.grid.minor = element_blank(),
- panel.border = element_blank(),
- legend.position="none",
- axis.line = element_blank(),
- axis.text.x = element_blank(),
- axis.text.y = element_text(size=10, face="bold", color = 'black'),
- axis.ticks=element_blank(),
- axis.title.x = element_blank(),
- axis.title.y = element_blank(),
- plot.title = element_blank()
- )
-
-
- both = rbind(ggplotGrob(p), ggplotGrob(data.table), size="last")
- panels <- both$layout$t[grep("panel", both$layout$name)]
- both$heights[panels] <- list(unit(1,"null"), unit(2, "lines"))
- both <- gtable_add_rows(both, heights = unit(1,"line"), 8)
- both <- gtable_add_grob(both,
- textGrob("Number at risk", hjust=0, x=0),
- t=9, l=2, r=4)
- plot_grid(both)
- } else {
- return(p)
- }
- }
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