From c3fecc1bf02818b037fca14dcc8cc34752358ced Mon Sep 17 00:00:00 2001
From: Jens Sauer <jsauer65@gmail.com>
Date: Mon, 16 Nov 2020 22:38:07 +0100
Subject: [PATCH] survival: Create functions for plots

Each plot has now its own function. This makes it easier to adjust the
creation and tweaking of a single plot. sma_plot_file() will now call
the individual plot function before saveing the plot.
---
 survival.R | 84 ++++++++++++++++++++++++++----------------------------
 utils.R    | 11 ++-----
 2 files changed, 42 insertions(+), 53 deletions(-)

diff --git a/survival.R b/survival.R
index 5bc657f..3b5b0eb 100644
--- a/survival.R
+++ b/survival.R
@@ -13,53 +13,49 @@ surv_dx <- Surv(time = secmal$event_time_dx, event = secmal$event_status)
 surv_asct <- Surv(time = secmal$event_time_asct, event = secmal$event_status)
 
 # plot survival after diagnosis
-# scaled to years
+sma_plot_surv_dx <- function() {
+	plot(survfit(surv_dx ~ 1), mark.time = TRUE, xscale = 365.25,
+	     xlab = "Years", ylab = "Survival")
+	title("Kaplan-Meier estimate for\nsecMalASCT study",
+	      "Survival after diagnosis")
+}
 
-sma_plot_file("survival_dx.png", png,
-		 list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
-		      sub = "Survival after diagnosis"),
-		 NULL,
-		 plot, survfit(surv_dx ~ 1),
-		 mark.time = TRUE,
-		 xscale = 365.25,
-		 xlab = "Years",
-		 ylab = "Survival")
+# plot survival after diagnosis per sex
+sma_plot_surv_dx_sex <- function() {
+	plot(survfit(surv_dx ~ sex, data = secmal), mark.time = TRUE,
+	     xscale = 365.25, xlab = "Years", ylab = "Survival",
+	     lty = 2:3)
+	title("Kaplan-Meier estimate for\nsecMalASCT study",
+	      "Survival after diagnosis")
+	legend(100, .9, c("Female", "Male"), lty = 2:3)
+}
 
 
-# One graph per sex
-sma_plot_file("survival_dx_sex.png", png,
-		 list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
-		      sub = "Survival after diagnosis"),
-		 list(100, .9, c("Female", "Male"), lty = 2:3),
-		 plot, survfit(surv_dx ~ sex, data = secmal),
-		 mark.time = TRUE,
-		 xscale = 365.25,
-		 xlab = "Years",
-		 ylab = "Survival",
-		 lty = 2:3)
+# plot survival after transplantation
+sma_plot_surv_asct <- function() {
+	plot(survfit(surv_asct ~ 1), mark.time = TRUE, xscale = 365.25,
+	     xlab = "Years", ylab = "Survival")
+	title("Kaplan-Meier estimate for\nsecMalASCT study",
+	      "Survival after transplantation")
+}
 
 
-# plot survival after diagnosis
-# scaled to years
-sma_plot_file("survival_asct.png", png,
-		 list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
-		      sub = "Survival after transplantation"),
-		 NULL,
-		 plot, survfit(surv_asct ~ 1),
-		 mark.time = TRUE,
-		 xscale = 365.25,
-		 xlab = "Years",
-		 ylab = "Survival")
+# plot survival after transplantation per sex
+sma_plot_surv_asct_sex <- function() {
+	plot(survfit(surv_asct ~ sex, data = secmal), mark.time = TRUE,
+	     xscale = 365.25, xlab = "Years", ylab = "Survival",
+	     lty = 2:3)
+	title("Kaplan-Meier estimate for\nsecMalASCT study",
+	      "Survival after transplantation")
+	legend(100, .9, c("Female", "Male"), lty = 2:3)
+}
 
-
-# One graph per sex
-sma_plot_file("survival_asct_sex.png", png,
-		 list(main = "Kaplan-Meier estimate for\nsecMalASCT study",
-		      sub = "Survival after transplantation"),
-		 list(100, .9, c("Female", "Male"), lty = 2:3),
-		 plot, survfit(surv_asct ~ sex, data = secmal),
-		 mark.time = TRUE,
-		 xscale = 365.25,
-		 xlab = "Years",
-		 ylab = "Survival",
-		 lty = 2:3)
+#
+# Write survival plots to files
+#
+sma_plot_file_surv <- function() {
+	sma_plot_file("survival_dx.png", png, sma_plot_surv_dx)
+	sma_plot_file("survival_dx_sex.png", png, sma_plot_surv_dx_sex)
+	sma_plot_file("survival_asct.png", png, sma_plot_surv_asct)
+	sma_plot_file("survival_asct_sex.png", png, sma_plot_surv_asct_sex)
+}
diff --git a/utils.R b/utils.R
index c8c6105..2972992 100644
--- a/utils.R
+++ b/utils.R
@@ -13,19 +13,12 @@ library(tidyverse)
 # or NULL if not needed.
 # Default filesize is 3000x3000 px and 300 dpi resolution.
 #
-sma_plot_file <- function(fname, ftype, title_list, legend_list, fun, ...) {
+sma_plot_file <- function(fname, ftype, fun) {
 	# Open file for writing
 	ftype(filename = fname, width = 3000, height = 3000, res = 300)
 
-	# run "fun" with passed arguments
-	do.call(fun, list(...))
+	fun()
 
-	if (!is.null(title_list)) {
-		do.call(title, title_list)
-	}
-	if(!is.null(legend_list)) {
-		do.call(legend, legend_list)
-	}
 	# hide "null device 1" in garbage
 	garbage <- dev.off()
 }