# Copyright 2019 Observational Health Data Sciences and Informatics
#
# This file is part of Argos
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#'saving tables and plot image which are the results incidence analysis
#'@param outputFolder
#'@param plot1yrsurvival
#'@param plot3yrsurvival
#'@param plot5yrsurvival
#'@param plottotalsurvival
#'@param imageExtension plot file's extension
#'@import ggplot2
#'@export
saveSurvival<-function(outputFolder,
plot1yrsurvival,
plot3yrsurvival,
plot5yrsurvival,
plottotalsurvival,
imageExtension = "png"){
ifelse(!dir.exists(file.path(outputFolder, "survival")), dir.create(file.path(outputFolder, "survival")), print("saving in survival folder"))
survivalFolder<-paste(outputFolder, "survival", sep = "/")
saveRDS(agedivSurvCal,file.path(survivalFolder,paste0("survivalData_cohortId_",cancerList$cohortId[[i]],".rds" )))
write.csv(agedivSurvCal,file.path(survivalFolder,paste0("survivalData_cohortId_",cancerList$cohortId[[i]],".csv" )))
saveRDS(totalSurvCal,file.path(survivalFolder,paste0("survivalData_Total_cohortId_",cancerList$cohortId[[i]],".rds" )))
write.csv(totalSurvCal,file.path(survivalFolder,paste0("survivalData_Total_cohortId_",cancerList$cohortId[[i]],".csv" )))
ggplot2::ggsave(file.path(survivalFolder, paste0(paste0(cancerList$cohortName[[i]],"Cancer", "1YrSurvivalRate"),".",imageExtension) ), plot1yrsurvival, width = 30,height = 10,units = "cm" )
ggplot2::ggsave(file.path(survivalFolder, paste0(paste0(cancerList$cohortName[[i]],"Cancer", "3YrSurvivalRate"),".",imageExtension) ), plot3yrsurvival, width = 30,height = 10,units = "cm" )
ggplot2::ggsave(file.path(survivalFolder, paste0(paste0(cancerList$cohortName[[i]],"Cancer", "5YrSurvivalRate"),".",imageExtension) ), plot5yrsurvival, width = 30,height = 10,units = "cm" )
ggplot2::ggsave(file.path(survivalFolder, paste0(paste0(cancerList$cohortName[[i]],"Cancer", "TotalSurvivalRate"),".",imageExtension) ), plottotalsurvival, width = 30,height = 10,units = "cm" )
}
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