--- a
+++ b/R/performance_analysis.R
@@ -0,0 +1,541 @@
+# performance_analysis.R
+
+require(data.table)
+require(ggplot2)
+
+
+plot_loss_by_bottleneck_and_split <- function(with_bottleneck_path, without_bottleneck_path, split_by_cell_path,
+                                 split_by_drug_path, split_by_both_path,
+                                 plot_path, cell_line_data, inference_results_paths, subtitle, plot_name) {
+  
+  
+  ctrp_data <- fread(paste0(path, "CTRP_AAC_MORGAN_512_inference_results.csv"))
+  ctrp_data <- merge(ctrp_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+  gdsc1_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+  gdsc1_data <- merge(gdsc1_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+  gdsc2_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_512_inference_results.csv"))
+  gdsc2_data <- merge(gdsc2_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+  
+  # ctrp_data[, abs_loss := sqrt(MSE_loss)]
+  ctrp_data[, lineage_loss_avg := mean(MAE_loss), by = "lineage"]
+  ctrp_data[, lineage_loss_sd := sd(MAE_loss), by = "lineage"]
+  ctrp_data[, sample_by_lineage_count := .N, by = "lineage"]
+  ctrp_avg_abs_by_lineage <- unique(ctrp_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+  ctrp_avg_abs_by_lineage$Dataset <- "CTRPv2"
+  
+  # gdsc1_data[, abs_loss := sqrt(MSE_loss)]
+  gdsc1_data[, lineage_loss_avg := mean(MAE_loss), by = "lineage"]
+  gdsc1_data[, lineage_loss_sd := sd(MAE_loss), by = "lineage"]
+  gdsc1_data[, sample_by_lineage_count := .N, by = "lineage"]
+  gdsc1_avg_abs_by_lineage <- unique(gdsc1_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+  gdsc1_avg_abs_by_lineage$Dataset <- "GDSC1"
+  
+  # gdsc2_data[, abs_loss := sqrt(MSE_loss)]
+  gdsc2_data[, lineage_loss_avg := mean(MAE_loss), by = "lineage"]
+  gdsc2_data[, lineage_loss_sd := sd(MAE_loss), by = "lineage"]
+  gdsc2_data[, sample_by_lineage_count := .N, by = "lineage"]
+  gdsc2_avg_abs_by_lineage <- unique(gdsc2_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+  gdsc2_avg_abs_by_lineage$Dataset <- "GDSC2"
+  
+  all_avg_abs_by_lineage <- rbindlist(list(ctrp_avg_abs_by_lineage, gdsc1_avg_abs_by_lineage, gdsc2_avg_abs_by_lineage))
+  all_avg_abs_by_lineage <- merge(all_avg_abs_by_lineage, unique(ctrp_data[, c("lineage", "sample_by_lineage_count")]))
+  all_avg_abs_by_lineage$lineage <- paste0(all_avg_abs_by_lineage$lineage, ", n = ", all_avg_abs_by_lineage$sample_by_lineage_count)
+  
+  ggplot(data = all_avg_abs_by_lineage, mapping = aes(x = reorder(lineage, -lineage_loss_avg), y = lineage_loss_avg, fill = Dataset)) +
+    geom_bar(stat = "identity", position = position_dodge()) +
+    # geom_errorbar(aes(ymin = lineage_loss_avg - lineage_loss_sd, ymax = lineage_loss_avg + lineage_loss_sd), width = 0.2, position = position_dodge(0.9)) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
+    geom_hline(yintercept = mean(ctrp_data$abs_loss), linetype="dashed", color = "red") +
+    # geom_text(aes(10, mean(ctrp_data$abs_loss),label = mean(ctrp_data$abs_loss), vjust = -1)) +
+    geom_hline(yintercept = mean(gdsc1_data$abs_loss), linetype="dashed", color = "green") +
+    geom_hline(yintercept = mean(gdsc2_data$abs_loss), linetype="dashed", color = "blue") +
+    xlab("Cell Line Lineage + # training datapoints") + ylab("Mean Absolute Loss") + 
+    # scale_y_discrete(limits = c("0.001", "0.002")) +
+    scale_y_continuous(breaks = sort(c(seq(0, 0.25, length.out=10),
+                                       c(mean(ctrp_data$abs_loss),
+                                         mean(gdsc1_data$abs_loss),
+                                         mean(gdsc2_data$abs_loss))
+    ))) +
+    # ggtitle(label = "Full DRP Mean Absolute Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on All 3")
+    ggtitle(label = title, subtitle = subtitle)
+  # ggsave(filename = paste0(plot_path, "drug_prot_train_CTRPv2_test_All_avg_Abs_by_lineage.pdf"), device = "pdf")
+  ggsave(filename = paste0(plot_path, plot_name), device = "pdf")
+  
+}
+
+
+plot_loss_by_lineage <- function(path,
+                                 plot_path, cell_line_data, title, subtitle, plot_filename, display_plot = FALSE) {
+  
+  cv_results <- fread(paste0(path, "CV_results.csv"))
+  cv_valid_loss <- cv_results[V1 == "avg_cv_valid_loss"][,2]
+  cv_valid_loss <- format(round(cv_valid_loss, 4), nsmall = 4)
+  ctrp_data <- fread(paste0(path, "CTRP_AAC_MORGAN_1024_inference_results.csv"))
+  ctrp_data <- merge(ctrp_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+  # gdsc1_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_1024_inference_results.csv"))
+  # gdsc1_data <- merge(gdsc1_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+  # gdsc2_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_1024_inference_results.csv"))
+  # gdsc2_data <- merge(gdsc2_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+  
+  # ctrp_data[, abs_loss := sqrt(MSE_loss)]
+  ctrp_data[, lineage_loss_avg := mean(RMSE_loss), by = "lineage"]
+  ctrp_data[, lineage_loss_sd := sd(RMSE_loss), by = "lineage"]
+  ctrp_data[, sample_by_lineage_count := .N, by = "lineage"]
+  ctrp_avg_abs_by_lineage <- unique(ctrp_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+  ctrp_avg_abs_by_lineage$Dataset <- "CTRPv2"
+  
+  # gdsc1_data[, lineage_loss_avg := mean(RMSE_loss), by = "lineage"]
+  # gdsc1_data[, lineage_loss_sd := sd(RMSE_loss), by = "lineage"]
+  # gdsc1_data[, sample_by_lineage_count := .N, by = "lineage"]
+  # gdsc1_avg_abs_by_lineage <- unique(gdsc1_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+  # gdsc1_avg_abs_by_lineage$Dataset <- "GDSC1"
+  # 
+  # gdsc2_data[, lineage_loss_avg := mean(RMSE_loss), by = "lineage"]
+  # gdsc2_data[, lineage_loss_sd := sd(RMSE_loss), by = "lineage"]
+  # gdsc2_data[, sample_by_lineage_count := .N, by = "lineage"]
+  # gdsc2_avg_abs_by_lineage <- unique(gdsc2_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+  # gdsc2_avg_abs_by_lineage$Dataset <- "GDSC2"
+  
+  # all_avg_abs_by_lineage <- rbindlist(list(ctrp_avg_abs_by_lineage, gdsc1_avg_abs_by_lineage, gdsc2_avg_abs_by_lineage))
+  all_avg_abs_by_lineage <- ctrp_avg_abs_by_lineage
+  all_avg_abs_by_lineage <- merge(all_avg_abs_by_lineage, unique(ctrp_data[, c("lineage", "sample_by_lineage_count")]))
+  all_avg_abs_by_lineage$lineage <- paste0(all_avg_abs_by_lineage$lineage, ", n = ", all_avg_abs_by_lineage$sample_by_lineage_count)
+  
+  g <- ggplot(data = all_avg_abs_by_lineage, mapping = aes(x = reorder(lineage, -lineage_loss_avg), y = lineage_loss_avg, fill = Dataset)) +
+    geom_bar(stat = "identity", position = position_dodge()) +
+    # geom_errorbar(aes(ymin = lineage_loss_avg - lineage_loss_sd, ymax = lineage_loss_avg + lineage_loss_sd), width = 0.2, position = position_dodge(0.9)) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
+    geom_hline(yintercept = mean(ctrp_data$lineage_loss_avg), linetype="dashed", color = "red") +
+    # geom_text(aes(10, mean(ctrp_data$abs_loss),label = mean(ctrp_data$abs_loss), vjust = -1)) +
+    # geom_hline(yintercept = mean(gdsc1_data$lineage_loss_avg), linetype="dashed", color = "green") +
+    # geom_hline(yintercept = mean(gdsc2_data$lineage_loss_avg), linetype="dashed", color = "blue") +
+    xlab("Cell Line Lineage + # testing datapoints") + ylab("RMSE Loss") + 
+    # scale_y_discrete(limits = c("0.001", "0.002")) +
+    scale_y_continuous(breaks = sort(c(seq(0, 0.25, length.out=10),
+                                       c(mean(ctrp_data$lineage_loss_avg)
+                                         # mean(gdsc1_data$lineage_loss_avg),
+                                         # mean(gdsc2_data$lineage_loss_avg)
+                                         )
+    ))) +
+    # ggtitle(label = "Full DRP Mean Absolute Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on All 3")
+    ggtitle(label = title, subtitle = paste0(subtitle, "\nAverage Cross-Validation RMSE Loss:", as.character(cv_valid_loss)))
+  if (display_plot == TRUE) {
+    print(g)
+  }
+  # ggsave(filename = paste0(plot_path, "drug_prot_train_CTRPv2_test_All_avg_Abs_by_lineage.pdf"), device = "pdf")
+  ggsave(plot = g, filename = paste0(plot_path, plot_filename), device = "pdf")
+  
+}
+# plot_path <- "Plots/DRP/Lineage_Results/"
+cell_line_data <- fread("Data/DRP_Training_Data/DepMap_21Q2_Line_Info.csv")
+
+
+plot_grid_mono <- function(model_type, data_type, split, bottleneck, drug_type) {
+  path <- paste0("Data/CV_Results/HyperOpt_DRP_", model_type, "_drug", data_type,
+                "_HyperOpt_DRP_CTRP_1024_", model_type, "_EncoderTrain_Split_", split, "_", bottleneck, "_NoTCGAPretrain_MergeBySum_RMSELoss_", drug_type, "_drug", data_type, "/")
+  # HyperOpt_DRP_ResponseOnly_drug_rppa_HyperOpt_DRP_CTRP_1024_ResponseOnly_EncoderTrain_Split_DRUG_NoBottleNeck_NoTCGAPretrain_MergeBySum_RMSELoss_OneHotDrugs_drug_rppa
+  if (split == "CELL_LINE") {
+    plot_path <- "Plots/DRP/Split_by_Cell/"
+    plot_split_name <- "SplitByCell"
+    title_split_name <- "Cell Line"
+  } else if (split == "DRUG") {
+    plot_path <- "Plots/DRP/Split_by_Drug/"
+    plot_split_name <- "SplitByDrug"
+    title_split_name <- "Drug"
+    
+  } else {
+    plot_path <- "Plots/DRP/Split_by_Both/"
+    plot_split_name <- "SplitByBoth"
+    title_split_name <- "Cell Line & Drug"
+    
+  }
+  if (bottleneck == "WithBottleNeck") {
+    subtitle_bottleneck_name <- "With Bottleneck"
+    
+  } else  {
+    subtitle_bottleneck_name <- "No Bottleneck"
+  }
+  
+  dir.create(plot_path)
+  plot_filename <- paste0(model_type, "_drug", data_type, "_train_CTRPv2_test_All_RMSE_", plot_split_name, "_", bottleneck, "_", drug_type, ".pdf")
+  title <- paste0("DRP RMSE (Validation by Strict ", title_split_name, " Splitting)")
+  subtitle <- paste0("Model Type: ", model_type, " | Data: Drug + ", gsub("_", "", toupper(data_type)), " | Drug Type: ", drug_type, " | Trained on CTRPv2 | Tested on All 3 | Hyper-Param Search: ", subtitle_bottleneck_name)
+  plot_loss_by_lineage(path = path, plot_path = plot_path, cell_line_data = cell_line_data, title = title, subtitle = subtitle, plot_filename = plot_filename)
+  
+}
+
+model_types <- c("FullModel", "ResponseOnly")
+data_types <- c("mut", "exp", "prot", "mirna", "metab", "rppa", "hist")
+data_types <- paste0("_", data_types)
+data_types <- c("", data_types)
+# splits <- c("CELL_LINE", "DRUG", "BOTH")
+splits <- c("DRUG")
+# bottlenecking <- c("WithBottleNeck", "NoBottleNeck")
+bottlenecking <- c("NoBottleNeck")
+drug_types <- c("OneHotDrugs")
+grid <- expand.grid(model_types, data_types, splits, bottlenecking, drug_types)
+
+for (i in 1:nrow(grid)) {
+  plot_grid_mono(model_type = grid[i, 1], data_type = grid[i, 2], split = grid[i, 3], bottleneck = grid[i, 4], drug_type = grid[i, 5])
+}
+
+# ==== Drug + Mut ====
+
+# Split by Cell, No Bottleneck
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_mut_HyperOpt_DRP_CTRP_FullModel_EncoderTrain_Split_CELL_LINE_NoBottleNeck_WithTCGAPretrain_drug_mut/"
+plot_path <- "Plots/DRP/Split_by_Cell/"
+dir.create(plot_path)
+plot_filename <- "drug_prot_train_CTRPv2_test_All_MAE_SplitByCell_NoBottleneck.pdf"
+subtitle <- "Data: Drug + Mutational | Trained on CTRPv2 | Tested on All 3 | Hyper-Param Search: No Bottleneck"
+title <- "Full DRP Mean Absolute Loss (Validation by Strict Cell Line Splitting)"
+plot_loss_by_lineage(path = path, plot_path = plot_path, cell_line_data = cell_line_data, title = title, subtitle = subtitle, plot_filename = plot_filename)
+
+# Split by Cell, With Bottleneck
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_mut_HyperOpt_DRP_CTRP_FullModel_EncoderTrain_Split_CELL_LINE_WithBottleNeck_WithTCGAPretrain_drug_mut/"
+plot_path <- "Plots/DRP/Split_by_Cell/"
+dir.create(plot_path)
+plot_filename <- "drug_prot_train_CTRPv2_test_All_MAE_SplitByCell_WithBottleneck.pdf"
+subtitle <- "Data: Drug + Mutational | Trained on CTRPv2 | Tested on All 3 | Hyper-Param Search: With Bottleneck"
+title <- "Full DRP Mean Absolute Loss (Validation by Strict Cell Line Splitting)"
+plot_loss_by_lineage(path = path, plot_path = plot_path, cell_line_data = cell_line_data, title = title, subtitle = subtitle, plot_filename = plot_filename)
+# ============
+# Split by Drug, No Bottleneck
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_mut_HyperOpt_DRP_CTRP_FullModel_EncoderTrain_Split_DRUG_NoBottleNeck_WithTCGAPretrain_drug_mut/"
+plot_path <- "Plots/DRP/Split_by_Drug/"
+dir.create(plot_path)
+plot_filename <- "drug_prot_train_CTRPv2_test_All_MAE_SplitByDrug_NoBottleneck.pdf"
+subtitle <- "Data: Drug + Mutational | Trained on CTRPv2 | Tested on All 3 | Hyper-Param Search: No Bottleneck"
+title <- "Full DRP Mean Absolute Loss (Validation by Strict Drug Splitting)"
+plot_loss_by_lineage(path = path, plot_path = plot_path, cell_line_data = cell_line_data, title = title, subtitle = subtitle, plot_filename = plot_filename)
+
+# Split by Drug, With Bottleneck
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_mut_HyperOpt_DRP_CTRP_FullModel_EncoderTrain_Split_DRUG_WithBottleNeck_WithTCGAPretrain_drug_mut/"
+plot_path <- "Plots/DRP/Split_by_Drug/"
+dir.create(plot_path)
+plot_filename <- "drug_prot_train_CTRPv2_test_All_MAE_SplitByDrug_WithBottleneck.pdf"
+subtitle <- "Data: Drug + Mutational | Trained on CTRPv2 | Tested on All 3 | Hyper-Param Search: With Bottleneck"
+title <- "Full DRP Mean Absolute Loss (Validation by Strict Drug Splitting)"
+plot_loss_by_lineage(path = path, plot_path = plot_path, cell_line_data = cell_line_data, title = title, subtitle = subtitle, plot_filename = plot_filename)
+# ============
+# Split by Drug, No Bottleneck
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_mut_HyperOpt_DRP_CTRP_FullModel_EncoderTrain_Split_BOTH_NoBottleNeck_WithTCGAPretrain_drug_mut/"
+plot_path <- "Plots/DRP/Split_by_Both/"
+dir.create(plot_path)
+plot_filename <- "drug_prot_train_CTRPv2_test_All_MAE_SplitByBoth_NoBottleneck.pdf"
+subtitle <- "Data: Drug + Mutational | Trained on CTRPv2 | Tested on All 3 | Hyper-Param Search: No Bottleneck"
+title <- "Full DRP Mean Absolute Loss (Validation by Strict Cell Line & Drug Splitting)"
+plot_loss_by_lineage(path = path, plot_path = plot_path, cell_line_data = cell_line_data, title = title, subtitle = subtitle, plot_filename = plot_filename)
+
+# Split by Drug, With Bottleneck
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_mut_HyperOpt_DRP_CTRP_FullModel_EncoderTrain_Split_BOTH_WithBottleNeck_WithTCGAPretrain_drug_mut/"
+plot_path <- "Plots/DRP/Split_by_Both/"
+dir.create(plot_path)
+plot_filename <- "drug_prot_train_CTRPv2_test_All_MAE_SplitByBoth_NoBottleneck.pdf"
+subtitle <- "Data: Drug + Mutational | Trained on CTRPv2 | Tested on All 3 | Hyper-Param Search: With Bottleneck"
+title <- "Full DRP Mean Absolute Loss (Validation by Strict Cell Line & Drug Splitting)"
+plot_loss_by_lineage(path = path, plot_path = plot_path, cell_line_data = cell_line_data, title = title, subtitle = subtitle, plot_filename = plot_filename)
+
+
+# 
+plot_path <- "Plots/DRP/Split_by_Drug/"
+plot_path <- "Plots/DRP/Split_by_Both/"
+plot_name <- ""
+# Plot average MSE by lineage Full (drug + prot) ================================
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_prot_CTRP_Full/"
+
+### GDSC1 ====
+cur_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on GDSC1")
+ggsave(filename = paste0(plot_path, "drug_prot_full_train_CTRPv2_test_GDSC1_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+### GDSC2 ====
+cur_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on GDSC2")
+ggsave(filename = paste0(plot_path, "drug_prot_full_train_CTRPv2_test_GDSC2_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+### CTRPv2 ====
+cur_data <- fread(paste0(path, "CTRP_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data = avg_mse_by_lineage) +
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on CTRPv2")
+ggsave(filename = paste0(plot_path, "drug_prot_train_CTRPv2_test_CTRP_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+### All side by side (lineage bar plot) ====
+ctrp_data <- fread(paste0(path, "CTRP_AAC_MORGAN_512_inference_results.csv"))
+ctrp_data <- merge(ctrp_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+gdsc1_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+gdsc1_data <- merge(gdsc1_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+gdsc2_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_512_inference_results.csv"))
+gdsc2_data <- merge(gdsc2_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+ctrp_data[, abs_loss := sqrt(MSE_loss)]
+ctrp_data[, lineage_loss_avg := mean(abs_loss), by = "lineage"]
+ctrp_data[, lineage_loss_sd := sd(abs_loss), by = "lineage"]
+ctrp_data[, sample_by_lineage_count := .N, by = "lineage"]
+ctrp_avg_abs_by_lineage <- unique(ctrp_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+ctrp_avg_abs_by_lineage$Dataset <- "CTRPv2"
+
+gdsc1_data[, abs_loss := sqrt(MSE_loss)]
+gdsc1_data[, lineage_loss_avg := mean(abs_loss), by = "lineage"]
+gdsc1_data[, lineage_loss_sd := sd(abs_loss), by = "lineage"]
+gdsc1_data[, sample_by_lineage_count := .N, by = "lineage"]
+gdsc1_avg_abs_by_lineage <- unique(gdsc1_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+gdsc1_avg_abs_by_lineage$Dataset <- "GDSC1"
+
+gdsc2_data[, abs_loss := sqrt(MSE_loss)]
+gdsc2_data[, lineage_loss_avg := mean(abs_loss), by = "lineage"]
+gdsc2_data[, lineage_loss_sd := sd(abs_loss), by = "lineage"]
+gdsc2_data[, sample_by_lineage_count := .N, by = "lineage"]
+gdsc2_avg_abs_by_lineage <- unique(gdsc2_data[, c("lineage", "lineage_loss_avg", "lineage_loss_sd")])
+gdsc2_avg_abs_by_lineage$Dataset <- "GDSC2"
+
+all_avg_abs_by_lineage <- rbindlist(list(ctrp_avg_abs_by_lineage, gdsc1_avg_abs_by_lineage, gdsc2_avg_abs_by_lineage))
+all_avg_abs_by_lineage <- merge(all_avg_abs_by_lineage, unique(ctrp_data[, c("lineage", "sample_by_lineage_count")]))
+all_avg_abs_by_lineage$lineage <- paste0(all_avg_abs_by_lineage$lineage, ", n = ", all_avg_abs_by_lineage$sample_by_lineage_count)
+
+ggplot(data = all_avg_abs_by_lineage, mapping = aes(x = reorder(lineage, -lineage_loss_avg), y = lineage_loss_avg, fill = Dataset)) +
+  geom_bar(stat = "identity", position = position_dodge()) +
+  # geom_errorbar(aes(ymin = lineage_loss_avg - lineage_loss_sd, ymax = lineage_loss_avg + lineage_loss_sd), width = 0.2, position = position_dodge(0.9)) +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
+  geom_hline(yintercept = mean(ctrp_data$abs_loss), linetype="dashed", color = "red") +
+  # geom_text(aes(10, mean(ctrp_data$abs_loss),label = mean(ctrp_data$abs_loss), vjust = -1)) +
+  geom_hline(yintercept = mean(gdsc1_data$abs_loss), linetype="dashed", color = "green") +
+  geom_hline(yintercept = mean(gdsc2_data$abs_loss), linetype="dashed", color = "blue") +
+  xlab("Cell Line Lineage + # training datapoints") + ylab("Average Absolute Loss") + 
+  # scale_y_discrete(limits = c("0.001", "0.002")) +
+  scale_y_continuous(breaks = sort(c(seq(0, 0.12, length.out=5),
+                                     c(mean(ctrp_data$abs_loss),
+                                       mean(gdsc1_data$abs_loss),
+                                       mean(gdsc2_data$abs_loss))
+  ))) +
+  ggtitle(label = "Full DRP Mean Absolute Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on All 3")
+ggsave(filename = paste0(plot_path, "drug_prot_train_CTRPv2_test_All_avg_Abs_by_lineage.pdf"), device = "pdf")
+
+
+### All side by side (cell line dot plot) ====
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_prot_CTRP_Full/"
+
+ctrp_data <- fread(paste0(path, "CTRP_AAC_MORGAN_512_inference_results.csv"))
+ctrp_data <- merge(ctrp_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+gdsc1_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+gdsc1_data <- merge(gdsc1_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+gdsc2_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_512_inference_results.csv"))
+gdsc2_data <- merge(gdsc2_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+ctrp_data[, lineage_loss_sd := sd(MSE_loss), by = "lineage"]
+ctrp_data[, cell_line_loss_avg := mean(MSE_loss), by = "cell_name"]
+ctrp_avg_mse_by_cell_line <- unique(ctrp_data[, c("cell_name", "lineage", "cell_line_loss_avg", "lineage_loss_sd")])
+ctrp_avg_mse_by_cell_line$Dataset <- "CTRPv2"
+
+gdsc1_data[, lineage_loss_sd := sd(MSE_loss), by = "lineage"]
+gdsc1_data[, cell_line_loss_avg := mean(MSE_loss), by = "cell_name"]
+gdsc1_avg_mse_by_cell_line <- unique(gdsc1_data[, c("cell_name", "lineage", "cell_line_loss_avg", "lineage_loss_sd")])
+gdsc1_avg_mse_by_cell_line$Dataset <- "GDSC1"
+
+gdsc2_data[, lineage_loss_sd := sd(MSE_loss), by = "lineage"]
+gdsc2_data[, cell_line_loss_avg := mean(MSE_loss), by = "cell_name"]
+gdsc2_avg_mse_by_cell_line <- unique(gdsc2_data[, c("cell_name", "lineage", "cell_line_loss_avg", "lineage_loss_sd")])
+gdsc2_avg_mse_by_cell_line$Dataset <- "GDSC2"
+
+all_avg_mse_by_cell_line <- rbindlist(list(ctrp_avg_mse_by_cell_line, gdsc1_avg_mse_by_cell_line, gdsc2_avg_mse_by_cell_line))
+ggplot(data = all_avg_mse_by_cell_line, mapping = aes(x = cell_name, y = cell_line_loss_avg, group = Dataset)) +
+  facet_wrap(vars(lineage), scales = "free") +
+  # geom_bar(stat = "identity", position = position_dodge()) +
+  # geom_dotplot(binaxis = 'y', stackdir = 'center') +
+  geom_boxplot() +
+  geom_errorbar(aes(ymin = cell_line_loss_avg - lineage_loss_sd, ymax = cell_line_loss_avg + lineage_loss_sd), width = 0.2, position = position_dodge(0.9)) +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
+  geom_hline(yintercept = mean(ctrp_data$MSE_loss), linetype="dashed", color = "red") +
+  # geom_text(aes(10, mean(ctrp_data$MSE_loss),label = mean(ctrp_data$MSE_loss), vjust = -1)) +
+  geom_hline(yintercept = mean(gdsc1_data$MSE_loss), linetype="dashed", color = "green") +
+  geom_hline(yintercept = mean(gdsc2_data$MSE_loss), linetype="dashed", color = "blue") +
+  xlab("Cell Line Lineage + # training datapoints") + ylab("Average MSE Loss") + 
+  # scale_y_discrete(limits = c("0.001", "0.002")) +
+  scale_y_continuous(breaks = sort(c(seq(0, 0.12, length.out=5),
+                                     c(mean(ctrp_data$MSE_loss),
+                                       mean(gdsc1_data$MSE_loss),
+                                       mean(gdsc2_data$MSE_loss))
+  ))) +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on All 3")
+ggsave(filename = paste0(plot_path, "drug_prot_train_CTRPv2_test_All_avg_MSE_by_cell_line.pdf"), device = "pdf")
+
+# Plot average MSE by lineage Full Response Only + EncoderTrain + PreTrain (drug + exp) ================================
+path = "Data/CV_Results/HyperOpt_DRP_ResponseOnly_drug_exp_CTRP_EncoderTrain_PreTrain/"
+
+### GDSC1
+cur_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "ResponseOnly DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on GDSC1")
+ggsave(filename = paste0(plot_path, "drug_prot_full_train_CTRPv2_test_GDSC1_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+### GDSC2
+cur_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on GDSC2")
+ggsave(filename = paste0(plot_path, "drug_prot_full_train_CTRPv2_test_GDSC2_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+### CTRPv2
+cur_data <- fread(paste0(path, "CTRP_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Proteomics | Trained on CTRPv2 | Tested on CTRPv2")
+ggsave(filename = paste0(plot_path, "drug_prot_train_CTRPv2_test_CTRP_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+# Plot average MSE by lineage (drug + exp) ================================
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_exp_CTRP_Full/"
+# GDSC1
+cur_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Gene Expression | Trained on CTRPv2 | Tested on GDSC1")
+ggsave(filename = paste0(plot_path, "drug_exp_train_CTRPv2_test_GDSC1_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+# Plot average MSE by lineage Full (drug + exp + prot) ================================
+path = "Data/CV_Results/HyperOpt_DRP_FullModel_drug_exp_prot_CTRP_Full/"
+### GDSC1 ====
+cur_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Gene Expression + Proteomics | Trained on CTRPv2 | Tested on GDSC1")
+ggsave(filename = paste0(plot_path, "drug_exp_prot_full_train_CTRPv2_test_GDSC1_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+# GDSC2
+cur_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Gene Expression + Proteomics | Trained on CTRPv2 | Tested on GDSC2")
+ggsave(filename = paste0(plot_path, "drug_exp_prot_full_train_CTRPv2_test_GDSC2_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+# CTRPv2
+cur_data <- fread(paste0(path, "CTRP_AAC_MORGAN_512_inference_results.csv"))
+cur_data <- merge(cur_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+cur_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+avg_mse_by_lineage <- unique(cur_data[, c("lineage", "lineage_loss_avg")])
+ggplot(data =  avg_mse_by_lineage)+
+  geom_bar(mapping = aes(x = reorder(lineage,-lineage_loss_avg), y = lineage_loss_avg), stat = "identity") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text()) + 
+  geom_hline(yintercept = mean(cur_data$MSE_loss), linetype="dashed", color = "red") +
+  xlab("Cell Line Lineage") + ylab("Average MSE Loss") +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Gene Expression + Proteomics | Trained on CTRPv2 | Tested on CTRPv2")
+ggsave(filename = paste0(plot_path, "drug_exp_prot_full_train_CTRPv2_test_CTRP_avg_MSE_by_lineage.pdf"), device = "pdf")
+
+
+### All side by side ====
+ctrp_data <- fread(paste0(path, "CTRP_AAC_MORGAN_512_inference_results.csv"))
+ctrp_data <- merge(ctrp_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+gdsc1_data <- fread(paste0(path, "GDSC1_AAC_MORGAN_512_inference_results.csv"))
+gdsc1_data <- merge(gdsc1_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+gdsc2_data <- fread(paste0(path, "GDSC2_AAC_MORGAN_512_inference_results.csv"))
+gdsc2_data <- merge(gdsc2_data, cell_line_data[, c("stripped_cell_line_name", "lineage")], by.x = "cell_name", by.y = "stripped_cell_line_name")
+
+ctrp_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+ctrp_avg_mse_by_lineage <- unique(ctrp_data[, c("lineage", "lineage_loss_avg")])
+ctrp_data[, sample_by_lineage_count := .N, by = "lineage"]
+ctrp_avg_mse_by_lineage$Dataset <- "CTRPv2"
+
+gdsc1_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+gdsc1_avg_mse_by_lineage <- unique(gdsc1_data[, c("lineage", "lineage_loss_avg")])
+gdsc1_avg_mse_by_lineage$Dataset <- "GDSC1"
+
+gdsc2_data[, lineage_loss_avg := mean(MSE_loss), by = "lineage"]
+gdsc2_avg_mse_by_lineage <- unique(gdsc2_data[, c("lineage", "lineage_loss_avg")])
+gdsc2_avg_mse_by_lineage$Dataset <- "GDSC2"
+
+all_avg_mse_by_lineage <- rbindlist(list(ctrp_avg_mse_by_lineage, gdsc1_avg_mse_by_lineage, gdsc2_avg_mse_by_lineage))
+all_avg_mse_by_lineage <- merge(all_avg_mse_by_lineage, unique(ctrp_data[, c("lineage", "sample_by_lineage_count")]))
+all_avg_mse_by_lineage$lineage <- paste0(all_avg_mse_by_lineage$lineage, ", n = ", all_avg_mse_by_lineage$sample_by_lineage_count)
+
+ggplot(data = all_avg_mse_by_lineage) +
+  geom_bar(mapping = aes(x = reorder(lineage, -lineage_loss_avg), y = lineage_loss_avg, fill = Dataset), stat = "identity", position = "dodge") +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
+  geom_hline(yintercept = mean(ctrp_data$MSE_loss), linetype="dashed", color = "red") +
+  # geom_text(aes(10, mean(ctrp_data$MSE_loss),label = mean(ctrp_data$MSE_loss), vjust = -1)) +
+  geom_hline(yintercept = mean(gdsc1_data$MSE_loss), linetype="dashed", color = "green") +
+  geom_hline(yintercept = mean(gdsc2_data$MSE_loss), linetype="dashed", color = "blue") +
+  xlab("Cell Line Lineage  + # training datapoints") + ylab("Average MSE Loss") + 
+  # scale_y_discrete(limits = c("0.001", "0.002")) +
+  scale_y_continuous(breaks = sort(c(seq(0, 0.12, length.out=5),
+                                     c(mean(ctrp_data$MSE_loss),
+                                       mean(gdsc1_data$MSE_loss),
+                                       mean(gdsc2_data$MSE_loss))
+  ))) +
+  ggtitle(label = "Full DRP Mean MSE Loss by Cell Line Lineage", subtitle = "Data: Drug + Expression + Proteomics | Trained on CTRPv2 | Tested on All 3")
+ggsave(filename = paste0(plot_path, "drug_exp_prot_train_CTRPv2_test_All_avg_MSE_by_lineage.pdf"), device = "pdf")
+