Merge pull request #24 from cyk0315/master

theme JAMA , NEJM
jinseob2kim · Jan 26, 2024 · dcd22d6 · dcd22d6
2 parents 8839bea + dd023eb
commit dcd22d6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,17 @@
 Package: jskm
 Title: Kaplan-Meier Plot with 'ggplot2'
-Version: 0.5.2
-Date: 2023-08-04
+Version: 0.5.3
+Date: 2024-01-24
 Authors@R: c(person("Jinseob", "Kim", email = "jinseob2kim@gmail.com", role = c("aut", "cre"),  comment = c(ORCID = "0000-0002-9403-605X")),
+             person("yoonkyoung", "Chun", email = "rachel200357@gmail.com"),
              person("Zarathu", role = c("cph", "fnd"))
              )
 Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator. 
 Depends: R (>= 3.4.0)
 License: Apache License 2.0  
 Encoding: UTF-8
-Imports: ggplot2, ggpubr, survival, survey, scales
-RoxygenNote: 7.2.3
+Imports: ggplot2, ggpubr, survival, survey, scales, patchwork
+RoxygenNote: 7.3.1
 URL: https://github.com/jinseob2kim/jskm
 BugReports: https://github.com/jinseob2kim/jstable/issues
 Suggests: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -30,6 +30,7 @@ importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(ggpubr,ggarrange)
 importFrom(grid,unit)
+importFrom(patchwork,inset_element)
 importFrom(stats,as.formula)
 importFrom(stats,formula)
 importFrom(stats,pchisq)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# jskm 0.5.3
+
+* Update: Add theme('JAMA','NEJM') to `jskm` and `svyjskm`
+
 # jskm 0.5.2
 
 * Update: Add `linewidth` option

diff --git a/R/jskm.R b/R/jskm.R
@@ -33,6 +33,10 @@
 #' @param showpercent Shows the percentages on the right side.
 #' @param status.cmprsk Status value when competing risk analysis, Default = 2nd level of status variable
 #' @param linewidth Line witdh, Default = 0.75
+#' @param theme Theme of the plot, Default = NULL, "nejm" for NEJMOA style, "jama" for JAMA style
+#' @param nejm.infigure.ratiow Ratio of infigure width to total width, Default = 0.6
+#' @param nejm.infigure.ratioh Ratio of infigure height to total height, Default = 0.5
+#' @param nejm.infigure.ylim y-axis limit of infigure, Default = c(0,1)
 #' @param ... PARAM_DESCRIPTION
 #' @return Plot
 #' @details DETAILS
@@ -73,6 +77,7 @@
 #' @importFrom grid unit
 #' @importFrom ggpubr ggarrange
 #' @importFrom stats pchisq time as.formula
+#' @importFrom patchwork inset_element
 #' @importFrom survival survfit survdiff coxph Surv cluster frailty
 #' @export
 
@@ -110,6 +115,11 @@ jskm <- function(sfit,
                  showpercent = F,
                  status.cmprsk = NULL,
                  linewidth = 0.75,
+                 theme=NULL,
+                 nejm.infigure.ratiow=0.6,
+                 nejm.infigure.ratioh=0.5,
+                 nejm.infigure.ylim=c(0,1),
+
                  ...) {
   #################################
   # sorting the use of subsetting #
@@ -118,7 +128,7 @@ jskm <- function(sfit,
   n.risk <- n.censor <- surv <- strata <- lower <- upper <- NULL
 
   times <- seq(0, max(sfit$time), by = timeby)
-
+  if(!is.null(theme)&&theme=='nejm') legendposition<-'right'
   if (is.null(subs)) {
     if (length(levels(summary(sfit)$strata)) == 0) {
       subs1 <- 1
@@ -148,43 +158,43 @@ jskm <- function(sfit,
     subs2 <- which(regexpr(ssvar, summary(sfit, censored = T)$strata, perl = T) != -1)
     subs3 <- which(regexpr(ssvar, summary(sfit, times = times, extend = TRUE)$strata, perl = T) != -1)
   }
-
+  
   if (!is.null(subs) | !is.null(sfit$states)) pval <- FALSE
-
+  
   ##################################
   # data manipulation pre-plotting #
   ##################################
-
+  
   if (is.null(ylabs)) {
     if (cumhaz | !is.null(sfit$states)) {
       ylabs <- "Cumulative incidence"
     } else {
       ylabs <- "Survival probability"
     }
   }
-
-
+  
+  
   if (length(levels(summary(sfit)$strata)) == 0) {
     # [subs1]
     if (is.null(ystratalabs)) ystratalabs <- as.character(sub("group=*", "", "All"))
   } else {
     # [subs1]
     if (is.null(ystratalabs)) ystratalabs <- as.character(sub("group=*", "", names(sfit$strata)))
   }
-
+  
   if (is.null(ystrataname)) ystrataname <- "Strata"
   m <- max(nchar(ystratalabs))
   times <- seq(0, max(sfit$time), by = timeby)
-
+  
   if (length(levels(summary(sfit)$strata)) == 0) {
     Factor <- factor(rep("All", length(subs2)))
   } else {
     Factor <- factor(summary(sfit, censored = T)$strata[subs2], levels = names(sfit$strata))
   }
-
+  
   # Data to be used in the survival plot
-
-
+  
+  
   if (is.null(sfit$state)) { # no cmprsk
     df <- data.frame(
       time = sfit$time[subs2],
@@ -316,8 +326,8 @@ jskm <- function(sfit,
   scale_labels <- ggplot2::waiver()
   if (surv.scale == "percent") scale_labels <- scales::percent
 
-  p <- ggplot2::ggplot(df, aes(x = time, y = surv, colour = strata, linetype = strata)) +
-    ggtitle(main)
+  p <- ggplot2::ggplot(df, aes(x = time, y = surv, colour = strata, linetype = strata) ) + ggtitle(main)
+
 
   linecols2 <- linecols
   if (linecols == "black") {
@@ -333,19 +343,26 @@ jskm <- function(sfit,
       axis.title.x = element_text(vjust = 0.7),
       panel.grid.minor = element_blank(),
       axis.line = element_line(linewidth = 0.5, colour = "black"),
-      legend.position = legendposition,
-      legend.background = element_rect(fill = NULL),
+    legend.position = legendposition,
+     legend.background = element_rect(fill = NULL),
       legend.key = element_rect(colour = NA),
       panel.border = element_blank(),
       plot.margin = unit(c(0, 1, .5, ifelse(m < 10, 1.5, 2.5)), "lines"),
-      panel.grid.major = element_blank(),
       axis.line.x = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
       axis.line.y = element_line(linewidth = 0.5, linetype = "solid", colour = "black")
     ) +
     scale_x_continuous(xlabs, breaks = times, limits = xlims) +
     scale_y_continuous(ylabs, limits = ylims, labels = scale_labels)
-
-
+
+  if(!is.null(theme)&&theme=='jama'){
+    p<-p+theme(
+      panel.grid.major.x = element_blank()
+    )
+  } else{
+    p <- p + theme(
+      panel.grid.major = element_blank()
+    )}
+
 
   # Removes the legend:
   if (legend == FALSE) {
@@ -355,13 +372,18 @@ jskm <- function(sfit,
   # Add lines too plot
   if (is.null(cut.landmark)) {
     p <- p + geom_step(linewidth = linewidth) +
-      scale_linetype_manual(name = ystrataname, values = linetype) +
-      scale_colour_brewer(name = ystrataname, palette = linecols)
+      scale_linetype_manual(name = ystrataname, values = linetype)    
   } else {
     p <- p +
       scale_linetype_manual(name = ystrataname, values = linetype) +
-      geom_step(data = subset(df, time >= cut.landmark), linewidth = linewidth) + geom_step(data = subset(df, time < cut.landmark), linewidth = linewidth) +
-      scale_colour_brewer(name = ystrataname, palette = linecols)
+      geom_step(data = subset(df, time >= cut.landmark), linewidth = linewidth) + geom_step(data = subset(df, time < cut.landmark), linewidth = linewidth) 
+  }
+
+  if(!is.null(theme)&&theme=='jama'){
+    p<-p+scale_color_manual(name=ystrataname, values = c("#00AFBB", "#E7B800", "#FC4E07"))
+  }else{  
+    p<-p+ scale_colour_brewer(name = ystrataname, palette = linecols)
+
   }
 
 
@@ -382,7 +404,7 @@ jskm <- function(sfit,
   if (!is.null(cut.landmark)) {
     p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
   }
-
+  p1<-p
   if (showpercent == T) {
     if (is.null(cut.landmark)) {
       y.percent <- summary(sfit, times = xlims[2], extend = T)$surv
@@ -391,7 +413,11 @@ jskm <- function(sfit,
       }
       if (cumhaz == T & is.null(sfit$states)) y.percent <- 1 - y.percent
       p <- p + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black")
-    } else {
+      if(!is.null(theme)&&theme == 'nejm') {
+        p1 <- p1 + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black",size=nejm.infigure.ratiow*5)
+
+      }
+        } else {
       y.percent1 <- summary(sfit, times = cut.landmark, extend = T)$surv
       y.percent2 <- summary(sfit2, times = xlims[2], extend = T)$surv
       if (!is.null(sfit$states)) {
@@ -404,7 +430,12 @@ jskm <- function(sfit,
       }
       p <- p + annotate(geom = "text", x = cut.landmark, y = y.percent1, label = paste0(round(100 * y.percent1, 1), "%"), color = "black") +
         annotate(geom = "text", x = xlims[2], y = y.percent2, label = paste0(round(100 * y.percent2, 1), "%"), color = "black")
-    }
+      if(!is.null(theme)&&theme == 'nejm') {
+        p1 <- p1 + annotate(geom = "text", x = cut.landmark, y = y.percent1, label = paste0(round(100 * y.percent1, 1), "%"), color = "black",size=nejm.infigure.ratiow*5) +
+          annotate(geom = "text", x = xlims[2], y = y.percent2, label = paste0(round(100 * y.percent2, 1), "%"), color = "black",size=nejm.infigure.ratiow*5)
+
+      }
+       }
   }
 
 
@@ -425,7 +456,7 @@ jskm <- function(sfit,
 
   if (length(levels(summary(sfit)$strata)) == 0) pval <- F
   # if(!is.null(cut.landmark)) pval <- F
-
+  
   if (pval == TRUE) {
     if (is.null(data)) {
       data <- tryCatch(eval(sfit$call$data), error = function(e) e)
@@ -453,7 +484,7 @@ jskm <- function(sfit,
 
       pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
       if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
-
+      
       # MOVE P-VALUE LEGEND HERE BELOW [set x and y]
       if (is.null(pval.coord)) {
         p <- p + annotate("text", x = (as.integer(max(sfit$time) / 5)), y = 0.1 + ylims[1], label = pvaltxt, size = pval.size)
@@ -489,7 +520,7 @@ jskm <- function(sfit,
       pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
 
       if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
-
+      
       if (is.null(pval.coord)) {
         p <- p + annotate("text", x = c(as.integer(max(sfit$time) / 10), as.integer(max(sfit$time) / 10) + cut.landmark), y = 0.1 + ylims[1], label = pvaltxt, size = pval.size)
       } else {
@@ -545,13 +576,22 @@ jskm <- function(sfit,
   #######################
   # Plotting the graphs #
   #######################
-
+
+  if(!is.null(theme)&&theme == 'nejm') {
+    p2<-p1+coord_cartesian(ylim=nejm.infigure.ylim)+theme(legend.position='none',axis.title.x = element_blank(),axis.title.y=element_blank(),
+                                                          axis.text= element_text(size=10*nejm.infigure.ratiow))
+    p<- p + patchwork::inset_element(p2, 1-nejm.infigure.ratiow,1-nejm.infigure.ratioh, 1, 1,align_to = 'panel')
+  }
+
   if (table == TRUE) {
     ggpubr::ggarrange(p, blank.pic, data.table,
-      nrow = 3, align = "v",
+      nrow = 3, 
+      #align = "v",
       heights = c(2, .1, .25)
     )
   } else {
-    p
+    p 
   }
 }
+
+