diff dose_response.R @ 1:8a1b524ed9d8 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit dca5f947ae4c9697ac0cfce0b313170b541124e5

--- a/dose_response.R	Mon Jun 10 11:57:52 2024 +0000
+++ b/dose_response.R	Tue Oct 08 12:41:07 2024 +0000
@@ -45,10 +45,14 @@
             plot.background = element_rect(fill = "white", color = NA)
         )
 
-    ggsave(filename = plot_file, plot = p, device = "jpg")
+    jpeg(filename = plot_file)
+    print(p)
+    dev.off()
 }
 
 dose_response_analysis <- function(data, concentration_col, response_col, plot_file, ec_file) {
+    concentration_col <- colnames(data)[as.integer(concentration_col)]
+    response_col <- colnames(data)[as.integer(response_col)]
     models <- fit_models(data, concentration_col, response_col)
     best_model_info <- select_best_model(models)
     ec_values <- calculate_ec_values(best_model_info$model)
@@ -59,7 +63,7 @@
         EC25 = ec_values$EC25[1],
         EC50 = ec_values$EC50[1]
     )
-    write.csv(ec_data, ec_file, row.names = FALSE)
+    write.table(ec_data, ec_file, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)
 
     return(list(best_model = best_model_info$name, ec_values = ec_values))
 }
@@ -72,5 +76,5 @@
 plot_file <- args[4]
 ec_file <- args[5]
 
-data <- read.csv(data_file, header = TRUE)
+data <- read.csv(data_file, header = TRUE, sep = "\t")
 dose_response_analysis(data, concentration_col, response_col, plot_file, ec_file)