fix readme

jinseob2kim · Jan 25, 2024 · dd023eb · dd023eb
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commit dd023eb
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Showing 6 changed files with 33 additions and 14 deletions.
diff --git a/R/jskm.R b/R/jskm.R
@@ -404,7 +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)$surv
@@ -413,7 +413,11 @@ jskm <- function(sfit,
       }
       if (cumhaz == T & is.null(sfit$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)) {
@@ -426,7 +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)
+
+      }
+       }
   }
 
 
@@ -447,7 +456,7 @@ jskm <- function(sfit,
 
   if (length(levels(summary(sfit)$strata)) == 0) pval <- F
   # if(!is.null(cut.landmark)) pval <- F
-  p1<-p
+
   if (pval == TRUE) {
     if (is.null(data)) {
       data <- tryCatch(eval(sfit$call$data), error = function(e) e)
@@ -569,7 +578,8 @@ jskm <- function(sfit,
   #######################
 
   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())
+    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')
   }
 

diff --git a/R/svyjskm.R b/R/svyjskm.R
@@ -334,23 +334,31 @@ svyjskm <- function(sfit,
   if (!is.null(cut.landmark)) {
     p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
   }
-
+
+  p1<-p
   ## p-value
   if (inherits(sfit, "svykm")) pval <- FALSE
   # if(is.null(design)) pval <- FALSE
   if (showpercent == TRUE) {
     if (is.null(cut.landmark)) {
       y.percent <- df[df$time %in% tapply(df$time, df$strata, max), "surv"]
       p <- p + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black")
-    } else {
+      if(!is.null(theme)&&theme == 'nejm') {
+        p1 <- p1 + annotate(geom = "text", x = xlims[2], y = y.percent, label = paste0(round(100 * y.percent, 1), "%"), color = "black",size=nejm.infigure.ratiow*5)
+      }
+      } else {
       df.cut <- df[df$time < cut.landmark, ]
       y.percent1 <- df.cut[df.cut$time %in% tapply(df.cut$time, df.cut$strata, max), "surv"]
       y.percent2 <- df[df$time %in% tapply(df$time, df$strata, max), "surv"]
       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)
+
+      }
+      }
   }
-  p1<-p
   if (pval) {
     if (is.null(design)) {
       design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
@@ -520,7 +528,8 @@ svyjskm <- 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())
+    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')
   }
 

diff --git a/README.Rmd b/README.Rmd
@@ -88,7 +88,7 @@ jskm(fit, theme='jama', cumhaz = T, table=T, mark = F, ylab = "Cumulative incide
 #### NEJM
 
 ```{r}
-jskm(fit, theme='nejm', nejm.infigure.ratiow = 0.6, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0,0.7), cumhaz = T, table=T, mark = F, ylab = "Cumulative incidence (%)", surv.scale = "percent", pval =T, pval.size = 6, pval.coord = c(300, 0.7))
+jskm(fit, theme='nejm', nejm.infigure.ratiow = 0.7, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0,0.7), cumhaz = T, table=T, mark = F, ylab = "Cumulative incidence (%)", surv.scale = "percent", pval =T, pval.size = 6, pval.coord = c(300, 0.7))
 ```
 
 ### Weighted Kaplan-Meier plot - `svykm.object` in **survey** package
@@ -129,5 +129,5 @@ svyjskm(s2, theme='jama', pval = T,  table = T, design = dpbc)
 #### NEJM
 
 ```{r}
-svyjskm(s2, theme='nejm', nejm.infigure.ratiow = 0.4, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0.2,1), pval = T,  table = T, design = dpbc)
+svyjskm(s2, theme='nejm', nejm.infigure.ratiow = 0.45, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0.2,1), pval = T,  table = T, design = dpbc)
 ```
diff --git a/README.md b/README.md
@@ -112,7 +112,7 @@ jskm(fit, theme='jama', cumhaz = T, table=T, mark = F, ylab = "Cumulative incide
 #### NEJM
 
 ``` r
-jskm(fit, theme='nejm', nejm.infigure.ratiow = 0.6, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0,0.7), cumhaz = T, table=T, mark = F, ylab = "Cumulative incidence (%)", surv.scale = "percent", pval =T, pval.size = 6, pval.coord = c(300, 0.7))
+jskm(fit, theme='nejm', nejm.infigure.ratiow = 0.7, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0,0.7), cumhaz = T, table=T, mark = F, ylab = "Cumulative incidence (%)", surv.scale = "percent", pval =T, pval.size = 6, pval.coord = c(300, 0.7))
 ```
 
 ![](man/figures/README-unnamed-chunk-6-1.png)<!-- -->
@@ -183,7 +183,7 @@ svyjskm(s2, theme='jama', pval = T,  table = T, design = dpbc)
 #### NEJM
 
 ``` r
-svyjskm(s2, theme='nejm', nejm.infigure.ratiow = 0.4, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0.2,1), pval = T,  table = T, design = dpbc)
+svyjskm(s2, theme='nejm', nejm.infigure.ratiow = 0.45, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0.2,1), pval = T,  table = T, design = dpbc)
 ```
 
 ![](man/figures/README-unnamed-chunk-10-1.png)<!-- -->
diff --git a/man/figures/README-unnamed-chunk-10-1.png b/man/figures/README-unnamed-chunk-10-1.png
diff --git a/man/figures/README-unnamed-chunk-6-1.png b/man/figures/README-unnamed-chunk-6-1.png