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

library(tidyverse)

#
# 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) {
	# Open file for writing
	ftype(filename = fname, width = 3000, height = 3000, res = 300)

	fun()

	# 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)

	return(sma)
}