From fcd2d330aae6dbed3b3210cedaba4cfb42de91b5 Mon Sep 17 00:00:00 2001
From: Jens Sauer <jsauer65@gmail.com>
Date: Tue, 17 Nov 2020 18:08:45 +0100
Subject: [PATCH] Add secondary malignancy plots

This adds some plots to show data for the secondary malignacies.
---
 .gitignore |  2 +-
 README.md  |  5 ++++
 secmal.R   | 87 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 93 insertions(+), 1 deletion(-)
 create mode 100644 secmal.R

diff --git a/.gitignore b/.gitignore
index ca5938d..f49da9a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,4 @@
 .RData
 .Rhistory
-survival_*
+*.png
 *.csv
diff --git a/README.md b/README.md
index 399de6b..282a288 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,11 @@ survival.R
 Source this file and call one of the plot functions to show plot in R.
 `sma_plot_file_surv()` will save all plots to files.
 
+secmal.R
+--------
+This file contains the secondary malignancy plots. You can call the
+functions in R or `sma_plot_file_secmal()` to save them to files.
+
 plot_survival.R
 ---------------
 Special script to generate all plots and save them in files.
diff --git a/secmal.R b/secmal.R
new file mode 100644
index 0000000..157787e
--- /dev/null
+++ b/secmal.R
@@ -0,0 +1,87 @@
+# Secondary malignancies calculations
+#
+# License: GPL version 3
+# Jens Mathis Sauer (c) 2020
+
+source("utils.R")
+sma_init()
+
+# Setup survival object
+surv_sec <- Surv(time = secmal$time_at_risk, event = secmal$time_at_risk_status)
+
+# plot cummulative events
+sma_plot_secmal_event <- function() {
+	ggsurvplot(survfit(surv_sec ~ 1), data = secmal, xscale = "d_y",
+		   title = "Secondary malignacies",
+		   fun = "event",
+		   break.time.by = sma_break.time.by,
+		   surv.median.line = "hv",
+		   risk.table = "nrisk_cumevents",
+		   ggtheme = theme_bw())
+}
+
+# plot cummulative hazard
+sma_plot_secmal_haz <- function() {
+	ggsurvplot(survfit(surv_sec ~ 1), data = secmal, xscale = "d_y",
+		   title = "Secondary malignacies",
+		   fun = "cumhaz",
+		   break.time.by = sma_break.time.by,
+		   risk.table = "abs_pct",
+		   ggtheme = theme_bw())
+}
+
+# plot cummulative events per sex
+sma_plot_secmal_event_sex <- function() {
+	ggsurvplot(survfit(surv_sec ~ sex, data = secmal), data = secmal, xscale = "d_y",
+		   title = "Secondary malignacies",
+		   fun = "event",
+		   break.time.by = sma_break.time.by,
+		   surv.median.line = "hv",
+		   risk.table = "nrisk_cumevents",
+		   pval = TRUE,
+		   ggtheme = theme_bw())
+}
+
+# plot cummulative hazard per sex
+sma_plot_secmal_haz_sex <- function() {
+	ggsurvplot(survfit(surv_sec ~ sex, data = secmal), data = secmal, xscale = "d_y",
+		   title = "Secondary malignacies",
+		   fun = "cumhaz",
+		   surv.median.line = "hv",
+		   break.time.by = sma_break.time.by,
+		   risk.table = "abs_pct",
+		   pval = TRUE,
+		   ggtheme = theme_bw())
+}
+
+# plot cummulative events per diagnosis
+sma_plot_secmal_event_dx <- function() {
+	ggsurvplot(survfit(surv_sec ~ diagnosis, data = secmal), data = secmal, xscale = "d_y",
+		   title = "Secondary malignacies",
+		   fun = "event",
+		   break.time.by = sma_break.time.by,
+		   risk.table = "nrisk_cumevents",
+		   pval = TRUE,
+		   ggtheme = theme_bw())
+}
+
+# plot cummulative hazard per diagnosis
+sma_plot_secmal_haz_dx <- function() {
+	ggsurvplot(survfit(surv_sec ~ diagnosis, data = secmal), data = secmal, xscale = "d_y",
+		   title = "Secondary malignacies",
+		   fun = "cumhaz",
+		   break.time.by = sma_break.time.by,
+		   risk.table = "abs_pct",
+		   pval = TRUE,
+		   ggtheme = theme_bw())
+}
+
+# Write secondary malignancy plots to files
+sma_plot_file_secmal <- function() {
+	sma_plot_file("secmal_event.png", png, sma_plot_secmal_event)
+	sma_plot_file("secmal_haz.png", png, sma_plot_secmal_haz)
+	sma_plot_file("secmal_event_sex.png", png, sma_plot_secmal_event_sex)
+	sma_plot_file("secmal_haz_sex.png", png, sma_plot_secmal_haz_sex)
+	sma_plot_file("secmal_event_dx.png", png, sma_plot_secmal_event_dx)
+	sma_plot_file("secmal_haz_dx.png", png, sma_plot_secmal_haz_dx)
+}