Merge branch 'secmal'

* secmal:
  Rename plot_survival.R
  Add secondary malignancy plots
  Introduce initialization function

.gitignore

@@ -1,4 +1,4 @@
 .RData
 .Rhistory
-survival_*
+*.png
 *.csv

README.md

@@ -10,10 +10,15 @@ 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.
 
-plot_survival.R
----------------
+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.
+
+plots.R
+-------
 Special script to generate all plots and save them in files.
-Run with `Rscript plot_survival.R`
+Run with `Rscript plots.R`
 
 Dependencies
 ------------

plots.R

@@ -1,10 +1,12 @@
-# secMalASCT survival plots
+# secMalASCT plots
 #
 # License: GPL version 3
 # Jens Mathis Sauer (c) 2020
 
 source("survival.R")
+source("secmal.R")
 
 #
 # Make all plots and save to file
 sma_plot_file_surv()
+sma_plot_file_secmal()

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)
+}

survival.R

@@ -3,11 +3,8 @@
 # License: GPL version 3
 # Jens Mathis Sauer (c) 2020
 
-library(survival)
-library(survminer)
 source("utils.R")
-
-secmal <- sma_load_data("current.csv")
+sma_init()
 
 # Setup survival object
 surv_dx <- Surv(time = secmal$event_time_dx, event = secmal$event_status)

utils.R

@@ -3,8 +3,6 @@
 # License: GPL version 3
 # Jens Mathis Sauer (c) 2020
 
-library(tidyverse)
-
 #
 # Write plot to filename
 #
@@ -86,3 +84,40 @@ sma_load_data <- function(file) {
 # Global break.time.by value
 #
 sma_break.time.by = 5 * 365.25
+
+#
+# Initialize secMalASCT workspace
+#
+# This function can be called multiple times, the data will only
+# be loaded once. To manually reload data call:
+# > sma_init_force()
+#
+sma_init <- function() {
+	if (exists("sma_initialized") == FALSE) {
+		print("Initialize secMalASCT workspace")
+
+		print("Loading libraries")
+		library(survival)
+		library(survminer)
+		library(tidyverse)
+
+		print("Loading data")
+		#
+		# Use superassignment operator '<<-' to make
+		# secmal and sma_initialized with global scope.
+		#
+		secmal <<- sma_load_data("current.csv")
+		sma_initialized <<- TRUE
+	}
+}
+
+#
+# Force reinitialization of workspace
+#
+# Forcefully calls sma_init() again.
+#
+sma_init_force <- function() {
+	print("Reloading secMalASCT data")
+	remove(sma_initialized, pos = ".GlobalEnv")
+	sma_init()
+}