Apply automatic stylistic changes

jinseob2kim · Apr 16, 2024 · 7114224 · 7114224
1 parent 38bb977
commit 7114224
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Showing 2 changed files with 19 additions and 15 deletions.
diff --git a/R/jskm.R b/R/jskm.R
@@ -380,20 +380,22 @@ jskm <- function(sfit,
       geom_step(data = subset(df, time >= cut.landmark), linewidth = linewidth) + geom_step(data = subset(df, time < cut.landmark), linewidth = linewidth)
   }
 
-  brewer.palette <- c("BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2", 
-                      "Set1", "Set2", "Set3", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples",
-                      "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd")
-
+  brewer.palette <- c(
+    "BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2",
+    "Set1", "Set2", "Set3", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples",
+    "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd"
+  )
+
   if (!is.null(theme) && theme == "jama") {
     col.pal <- c("#00AFBB", "#E7B800", "#FC4E07")
-    col.pal <- rep(col.pal, ceiling(length(ystratalabs)/3))
+    col.pal <- rep(col.pal, ceiling(length(ystratalabs) / 3))
   } else if (all(linecols %in% brewer.palette)) {
     col.pal <- NULL
   } else {
     col.pal <- linecols
-    col.pal <- rep(col.pal, ceiling(length(ystratalabs)/length(linecols)))
+    col.pal <- rep(col.pal, ceiling(length(ystratalabs) / length(linecols)))
   }
-  
+
   if (is.null(col.pal)) {
     p <- p + scale_colour_brewer(name = ystrataname, palette = linecols)
   } else {

diff --git a/R/svyjskm.R b/R/svyjskm.R
@@ -317,26 +317,28 @@ svyjskm <- function(sfit,
       scale_linetype_manual(name = ystrataname, values = linetype)
   }
 
-  brewer.palette <- c("BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2", 
-                      "Set1", "Set2", "Set3", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples",
-                      "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd")
-
+  brewer.palette <- c(
+    "BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2",
+    "Set1", "Set2", "Set3", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples",
+    "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd"
+  )
+
   if (!is.null(theme) && theme == "jama") {
     col.pal <- c("#00AFBB", "#E7B800", "#FC4E07")
-    col.pal <- rep(col.pal, ceiling(length(ystratalabs)/3))
+    col.pal <- rep(col.pal, ceiling(length(ystratalabs) / 3))
   } else if (all(linecols %in% brewer.palette)) {
     col.pal <- NULL
   } else {
     col.pal <- linecols
-    col.pal <- rep(col.pal, ceiling(length(ystratalabs)/length(linecols)))
+    col.pal <- rep(col.pal, ceiling(length(ystratalabs) / length(linecols)))
   }
-  
+
   if (is.null(col.pal)) {
     p <- p + scale_colour_brewer(name = ystrataname, palette = linecols)
   } else {
     p <- p + scale_color_manual(name = ystrataname, values = col.pal)
   }
-  
+
   # Add 95% CI to plot
   if (ci == TRUE) {
     if (all(linecols2 == "black")) {