# secMalASCT utilities
#
# License: GPL version 3
# Jens Mathis Sauer (c) 2020

library(survival)
library(survminer)
library(tidyverse)
library(cmprsk)
library(ggsci)

#
# Write plot to filename
#
# This will plot "fun" with arguments "..." as filetype "ftype" and
# the output to "filename". Title and legends can be passed as list,
# or NULL if not needed.
# Default filesize is 3000x3000 px and 300 dpi resolution.
#
sma_plot_file <- function(fname, ftype, fun, width = 4000, height = 3000) {
	# Open file for writing
	ftype(filename = fname, width = width, height = height, res = 300)

	#
	# Write plot into variable, then printing it manually. This is
	# needed to save plots from package "survminer" at the moment.
	#
	# See: https://github.com/kassambara/survminer/issues/152
	#
	p <- fun()
	print(p)

	# hide "null device 1" in garbage
	garbage <- dev.off()
}

#
# Load secMalASCT data
#
# This loads the secMalASCT data from a CSV file and adjusts some
# columns to the correct type.
#
sma_load_data <- function(file) {
	sma <- as_tibble(read.csv(file, header = TRUE))

	# Type adjustments
	sma$follow_up_multi <- as.logical(sma$follow_up_multi)
	sma$nicotin_history <- as.logical(sma$nicotin_history)
	sma$relapse_treatment_asct <- as.logical(sma$relapse_treatment_asct)
	sma$relapse_treatment_chemotherapy <- as.logical(sma$relapse_treatment_chemotherapy)
	sma$relapse_treatment_radiotherapy <- as.logical(sma$relapse_treatment_radiotherapy)
	sma$relapse_treatment_surgery <- as.logical(sma$relapse_treatment_surgery)

	sma$pre_rt <- as.logical(sma$pre_rt)
	sma$pre_rt_type <- as.factor(sma$pre_rt_type)
	sma$post_rt <- as.logical(sma$post_rt)
	sma$post_rt_type <- as.factor(sma$post_rt_type)

	sma$pre_alkylating_agents <- as.logical(sma$pre_alkylating_agents)
	sma$pre_topoisomerase <- as.logical(sma$pre_topoisomerase)
	sma$pre_anthracyclines <- as.logical(sma$pre_anthracyclines)

	sma$peri_alkylating_agents <- as.logical(sma$peri_alkylating_agents)
	sma$peri_topoisomerase <- as.logical(sma$peri_topoisomerase)
	sma$peri_anthracyclines <- as.logical(sma$peri_anthracyclines)

	sma$post_alkylating_agents <- as.logical(sma$post_alkylating_agents)
	sma$post_topoisomerase <- as.logical(sma$post_topoisomerase)
	sma$post_anthracyclines <- as.logical(sma$post_anthracyclines)

	sma$maintenance_treatment <- as.logical(sma$maintenance_treatment)
	sma$maintenance_treatment_time <- as.integer(sma$maintenance_treatment_time)
	sma$maintenance_treatment_type <- as.factor(sma$maintenance_treatment_type)

	sma$thalidomid <- as.logical(sma$thalidomid)
	sma$bortezomib <- as.logical(sma$bortezomib)

	#
	# Limit to patients which are at least 16.0 years old at time
	# of transplantation.
	sma <- filter(sma, asct_age >= 16.0)

	# At this time only solid tumors are important
	sma <- filter(sma, diagnosis_type == "solid")

	# Condense 'Ewing Sarcom'
	levels(sma$diagnosis)[match("Ewing sarcoma", levels(sma$diagnosis))] <- "Ewing sarcoma / PNET"

	# After filtering unused levels must be cleared from the data
	sma <- droplevels(sma)

	return(sma)
}

#
# 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 data")
		#
		# Use superassignment operator '<<-' to make
		# secmal and sma_initialized with global scope.
		#
		secmal <<- sma_load_data("data/data.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")
	remove(secmal, pos = ".GlobalEnv")
	sma_init()
}