fix t-test workflow for now, on/off has to be fixed later

Author: KarinSchork

R/Heatmap.R

@@ -213,6 +213,7 @@ Heatmap_with_groups <- function(D,
                 column_title_gp = grid::gpar(fontsize = textsize),
                 ...)
 
+  return(ht)
   #return(list("heatmap" = ht, "data_as_matrix" = cbind(id, data.asmatrix)))
 }
 

R/workflow_ttest.R

@@ -227,33 +227,33 @@ workflow_ttest <- function(data_path,
                                    groups = data[["group"]])
 
   grDevices::pdf(paste0(output_path, "heatmap", suffix, ".pdf"), height = plot_height, width = plot_width)
-  graphics::plot(t_heatmap[["heatmap"]])
+  graphics::plot(t_heatmap) # [["heatmap"]]
   grDevices::dev.off()
 
-  openxlsx::write.xlsx(cbind(data[["ID"]][candidates, ], zscore = t_heatmap[["data_as_matrix"]]), paste0(output_path, "heatmap_data", suffix, ".xlsx"), overwrite = TRUE, keepNA = TRUE)
+  #openxlsx::write.xlsx(cbind(data[["ID"]][candidates, ], zscore = t_heatmap[["data_as_matrix"]]), paste0(output_path, "heatmap_data", suffix, ".xlsx"), overwrite = TRUE, keepNA = TRUE)
 
   mess <- paste0(mess, "Heatmap made for the candidates. \n")
 
 
 
-  #### Create On-Off Heatmap ####
-
-  if(is.null(min_valid_values_on)){
-    min_valid_values_on <- length(intensity_columns)
-  }
-
-  t_on_off_heatmap <- calculate_onoff(D = data[["D"]],
-                                      id = data[["ID"]],
-                                      group = data[["group"]],
-                                      max_vv_off = max_valid_values_off,
-                                      min_vv_on = min_valid_values_on,
-                                      protein_id_col = 1)
-
-  grDevices::pdf(paste0(output_path, "on_off_heatmap", suffix, ".pdf"), height = plot_height, width = plot_width)
-  graphics::plot(t_on_off_heatmap)
-  grDevices::dev.off()
-
-  mess <- paste0(mess, "On-Off-Heatmap made. \n", "There were ", sum(t_on_off_heatmap[["isonoff"]]), " on/off proteins.")
+  # #### Create On-Off Heatmap ####
+  #
+  # if(is.null(min_valid_values_on)){
+  #   min_valid_values_on <- length(intensity_columns)
+  # }
+  #
+  # t_on_off_heatmap <- calculate_onoff(D = data[["D"]],
+  #                                     id = data[["ID"]],
+  #                                     group = data[["group"]],
+  #                                     max_vv_off = max_valid_values_off,
+  #                                     min_vv_on = min_valid_values_on,
+  #                                     protein_id_col = 1)
+  #
+  # grDevices::pdf(paste0(output_path, "on_off_heatmap", suffix, ".pdf"), height = plot_height, width = plot_width)
+  # graphics::plot(t_on_off_heatmap)
+  # grDevices::dev.off()
+  #
+  # mess <- paste0(mess, "On-Off-Heatmap made. \n", "There were ", sum(t_on_off_heatmap[["isonoff"]]), " on/off proteins.")