annotated figure 3a part in script

saezlab · Oct 7, 2022 · 4a9c22a · 4a9c22a
1 parent 1da7c4a
commit 4a9c22a
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Showing 2 changed files with 19 additions and 3 deletions.
diff --git a/figures/metabolomic_raw_violins.pdf b/figures/metabolomic_raw_violins.pdf
diff --git a/scripts/metabolomic/PLASMAX.R b/scripts/metabolomic/PLASMAX.R
@@ -223,8 +223,8 @@ translated_regulons_df$set <- gsub("___.*","",translated_regulons_df$ID)
 translated_regulons_df$targets <- gsub(".*___","",translated_regulons_df$ID)
 translated_regulons_df <- translated_regulons_df[,c(3,4,2)]
 
-##Visualise results for single enzmes
-plots <- plotMetaboliteContribution(enzyme = 'ASNS_glugln', stat_df = translated_results$t_table, 
+##Visualise results for single enzmes (Figure 3A)
+plots <- plotMetaboliteContribution(enzyme = 'BCAT1>780', stat_df = translated_results$t_table, 
                                     metabolite_sets = translated_regulons_df, 
                                     contrast_index = 1, stat_name = 'Abundance Down <==> Up (t-value)', 
                                     scaling_factor = 1, nLabels =  30)
@@ -233,13 +233,29 @@ plot(plots$scatter)
 # plot(plots$cumsumPlot)
 
 ##Visualise results for single enzmes
-plots <- plotMetaboliteContribution(enzyme = 'GRHPR', stat_df = translated_results$t_table, 
+plots <- plotMetaboliteContribution(enzyme = 'BCAT1>780', stat_df = translated_results$t_table, 
+                                    metabolite_sets = translated_regulons_df, 
+                                    contrast_index = 4, stat_name = 'Abundance Down <==> Up (t-value)', 
+                                    scaling_factor = 1, nLabels =  30)
+
+plot(plots$scatter)
+
+##Visualise results for single enzmes
+plots <- plotMetaboliteContribution(enzyme = 'BCAT1>780_gluakg', stat_df = translated_results$t_table, 
                                     metabolite_sets = translated_regulons_df, 
                                     contrast_index = 1, stat_name = 'Abundance Down <==> Up (t-value)', 
                                     scaling_factor = 1, nLabels =  30)
 
 plot(plots$scatter)
 
+##Visualise results for single enzmes
+plots <- plotMetaboliteContribution(enzyme = 'BCAT1>780_gluakg', stat_df = translated_results$t_table, 
+                                    metabolite_sets = translated_regulons_df, 
+                                    contrast_index = 4, stat_name = 'Abundance Down <==> Up (t-value)', 
+                                    scaling_factor = 1, nLabels =  30)
+
+plot(plots$scatter)
+
 ig_net <- graph_from_data_frame(sub_network_nocofact$reaction_network)
 
 shortest_paths(ig_net, from = "ADSL>2", to = "cpd:C00152_c", mode = "out")