modif order params

R/simulationreport.R

@@ -68,15 +68,15 @@ getGrobTable <- function(df){
 #'
 #' @param mock_obj A list containing simulation data and ground truth.
 #' @param list_tmb A list of model results.
-#' @param dds_obj a DESeq2 object
 #' @param coeff_threshold A threshold for comparing estimates.
 #' @param alt_hypothesis The alternative hypothesis for comparisons ("greater", "less", "greaterAbs").
 #' @param report_file File name to save the generated report. If NULL, the report will not be exported.
+#' @param dds_obj a DESeq2 object
 #' @importFrom ggplot2 aes geom_point geom_abline facet_wrap theme_bw ggtitle
 #' @return A list containing settings, plots, and evaluation results.
 #' @export
-simulationReport <- function(mock_obj, list_tmb = NULL, dds_obj = NULL ,
-                             coeff_threshold = 0, alt_hypothesis = "greaterAbs", report_file = NULL){
+simulationReport <- function(mock_obj, list_tmb = NULL,
+                             coeff_threshold = 0, alt_hypothesis = "greaterAbs", report_file = NULL, dds_obj = NULL ){
 
   #-- init 
   TMB_comparison_df <- data.frame()
@@ -111,12 +111,13 @@ simulationReport <- function(mock_obj, list_tmb = NULL, dds_obj = NULL ,
   comparison_df <- rbind( DESEQ_comparison_df, TMB_comparison_df )
   
   
-  color2use <- c("#D2B4DE", "#A2D9CE")
-  color2use <- color2use[c(!is.null(list_tmb), !is.null(dds_obj))]
+  #color2use <- c("#D2B4DE", "#A2D9CE")
+  color2use <- c("#500472", "#79cbb8")
+  color2use <- color2use[c(!is.null(dds_obj), !is.null(list_tmb))]
 
   # -- plotting
   roc_curve <- roc_plot(comparison_df, col = "from" ) + ggplot2::scale_color_manual(values = color2use)
-  id_plot <- identity_plot(comparison_df, col = "from") + ggplot2::scale_color_manual(values = color2use)
+  id_plot <- identity_plot(comparison_df, col = "from", pch = "from") + ggplot2::scale_color_manual(values = color2use)
   #metrics_plot <- metrics_plot(list_tmb)
   evalDisp <- evaluateDispersion(TMB_dispersion_df, DESEQ_dispersion_df, color2use )
   dispersion_plot <- evalDisp$disp_plot