upload

-# Based on http://www.sthda.com/english/wiki/ggplot2-line-plot-quick-start-guide-r-software-and-data-visualization
-
-library(ggplot2)
-#library(ggpubr)
-#library(cowplot)
-
-######### BEST MODELS ##########
-
-# Run1
-# Todas las condiciones
-dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=15),
-                Strategy=rep(c(
-                  "Agit",
-                  "Gversion",
-                  "Substrain",
-                  "Vess",
-                  "OD",
-                  "Anti",
-                  "Supp",
-                  "Air",
-                  "Gtype",
-                  "Med",
-                  "Temp",
-                  "Technique",
-                  "Phase",
-                  "pH",
-                  "Strain"
-                ),3),
-                Score=c(
-                  0,
-                  0,
-                  0,
-                  0,
-                  1,
-                  1,
-                  0.883,
-                  0.92,
-                  0.905,
-                  0.852,
-                  0.818,
-                  0.88,
-                  1,
-                  1,
-                  1,
-                  0,
-                  0,
-                  0,
-                  0,
-                  0.405,
-                  0.444,
-                  0.669,
-                  0.742,
-                  0.811,
-                  0.912,
-                  1,
-                  1,
-                  0.947,
-                  1,
-                  1,
-                  0,
-                  0,
-                  0,
-                  0,
-                  0.577,
-                  0.615,
-                  0.762,
-                  0.821,
-                  0.856,
-                  0.881,
-                  0.9,
-                  0.936,
-                  0.973,
-                  1,
-                  1
-                ))
-
-# Solo condiciones con F1-score > 0
-# Run 1
-df <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=11),
-                  Strategy=rep(c(
-                    "OD",
-                    "Anti",
-                    "Supp",
-                    "Air",
-                    "Gtype",
-                    "Med",
-                    "Temp",
-                    "Technique",
-                    "Phase",
-                    "pH",
-                    "Strain"
-                  ),3),
-                  Score=c(
-                    1,
-                    1,
-                    0.883,
-                    0.92,
-                    0.905,
-                    0.852,
-                    0.818,
-                    0.88,
-                    1,
-                    1,
-                    1,
-                    0.405,
-                    0.444,
-                    0.669,
-                    0.742,
-                    0.811,
-                    0.912,
-                    1,
-                    1,
-                    0.947,
-                    1,
-                    1,
-                    0.577,
-                    0.615,
-                    0.762,
-                    0.821,
-                    0.856,
-                    0.881,
-                    0.9,
-                    0.936,
-                    0.973,
-                    1,
-                    1
-                  ))
-
-head(df)
-
-pa<-ggplot(df, aes(x=Strategy, y=Score, group=Measure)) +
-  geom_line(aes(color=Measure))+
-  geom_point(aes(color=Measure))+
-  scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
-  #scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
-  #geom_text(aes(label = Score))+
-  labs(title="Scores by condition (Best model, Run1)",x="Condition", y = "Score")+
-  theme(
-    legend.position="top",
-    # Centrar título: plot.title = element_text(hjust = 0.5),
-    axis.line = element_line(colour = "gray"),
-    panel.background = element_blank(),
-    panel.grid.major = element_blank(),
-    panel.grid.minor = element_blank(),
-    panel.border = element_blank()
-  )
-pa
-
-ggsave(".png")
-
-# Solo condiciones con F1-score > 0
-# Run 7
-df <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=11),
-                 Strategy=rep(c(
-                   "Anti",
-                   "OD",
-                   "Supp",
-                   "Air",
-                   "Gtype",
-                   "Temp",
-                   "Med",
-                   "Technique",
-                   "Phase",
-                   "pH",
-                   "Strain"
-                 ),3),
-                 Score=c(
-                   0.571,
-                   1,
-                   0.886,
-                   0.939,
-                   0.876,
-                   0.818,
-                   0.897,
-                   0.952,
-                   1,
-                   1,
-                   1,
-                   0.444,
-                   0.405,
-                   0.684,
-                   0.742,
-                   0.802,
-                   1,
-                   0.912,
-                   0.909,
-                   0.947,
-                   1,
-                   1,
-                   0.5,
-                   0.577,
-                   0.772,
-                   0.829,
-                   0.837,
-                   0.9,
-                   0.904,
-                   0.93,
-                   0.973,
-                   1,
-                   1
-                 ))
-
-head(df)
-
-pa<-ggplot(df, aes(x=Strategy, y=Score, group=Measure)) +
-  geom_line(aes(color=Measure))+
-  geom_point(aes(color=Measure))+
-  scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
-  #scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
-  #geom_text(aes(label = Score))+
-  labs(title="Scores by condition (Best model, Run7)",x="Condition", y = "Score")+
-  theme(
-    legend.position="top",
-    # Centrar título: plot.title = element_text(hjust = 0.5),
-    axis.line = element_line(colour = "gray"),
-    panel.background = element_blank(),
-    panel.grid.major = element_blank(),
-    panel.grid.minor = element_blank(),
-    panel.border = element_blank()
-  )
-pa
-
-ggsave(".png")
-

-# Based on http://www.sthda.com/english/wiki/ggplot2-line-plot-quick-start-guide-r-software-and-data-visualization
-
-library(ggplot2)
-#library(ggpubr)
-#library(cowplot)
-
-######### BEST MODEL ##########
-
-# Solo condiciones con F1-score > 0
-# Run 6 (report_Run6_v11.txt)
-df <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=11),
-                  Strategy=rep(c(
-                    "Air", 
-                    "Anti", 
-                    "Gtype", 
-                    "Med", 
-                    "OD", 
-                    "pH", 
-                    "Phase", 
-                    "Supp", 
-                    "Technique", 
-                    "Temp", 
-                    "Vess"
-                  ),3),
-                  Score=c(
-                    0.565,
-                    1,
-                    0.889,
-                    1,
-                    1,
-                    1,
-                    0.882,
-                    0.811,
-                    1,
-                    0.923,
-                    1,
-                    0.377,
-                    1,
-                    0.847,
-                    0.943,
-                    0.818,
-                    1,
-                    1,
-                    0.799,
-                    0.913,
-                    0.828,
-                    1,
-                    0.452,
-                    1,
-                    0.867,
-                    0.971,
-                    0.9,
-                    1,
-                    0.938,
-                    0.805,
-                    0.955,
-                    0.873,
-                    1
-                  ))
-
-head(df)
-
-pa<-ggplot(df, aes(x=Strategy, y=Score, group=Measure)) +
-  geom_line(aes(color=Measure))+
-  geom_point(aes(color=Measure))+
-  scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
-  #scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
-  #geom_text(aes(label = Score))+
-  labs(title="Scores by condition (Best model, Run1)",x="Condition", y = "Score")+
-  theme(
-    legend.position="top",
-    # Centrar título: plot.title = element_text(hjust = 0.5),
-    axis.line = element_line(colour = "gray"),
-    panel.background = element_blank(),
-    panel.grid.major = element_blank(),
-    panel.grid.minor = element_blank(),
-    panel.border = element_blank()
-  )
-pa
-
-ggsave(".png")
-

-# Based on http://zevross.com/blog/2019/04/02/easy-multi-panel-plots-in-r-using-facet_wrap-and-facet_grid-from-ggplot2/
-
-library(ggplot2)
-#library(ggpubr)
-#library(cowplot)
-
-organism = 'ECO'
-
-if (organism == 'ECO') {
-######### ECO DEVELOPMENT DATASET ##########
-
-# ECO-DEV-WITH-EFFECT-COMBINATION: Combination of strategies with effect in E. coli development dataset
-df <- data.frame(Panel=rep(c("Combination of strategies (effect)", "Separated strategies (effect)", "Combination of strategies (no effect)", "Separated strategies (no effect)"), each=12),
-                Measure=rep(c("Precision", "Recall", "F1-score"), each=4),
-                Strategy=c(rep(c("D", "D+V", "D+V+At", "D+V+At+Au"),3),rep(c("D", "V", "At", "Au"),3)),
-                Score=c(
-                0.78, 0.79, 0.81, 0.81, 0.41, 0.56, 0.63, 0.63, 0.53, 0.65, 0.71, 0.71,
-                0.78, 0.89, 0.93, 1.00, 0.41, 0.35, 0.13, 0.01, 0.53, 0.50, 0.23, 0.02,
-                0.82, 0.82, 0.84, 0.84, 0.55, 0.66, 0.72, 0.72, 0.66, 0.73, 0.78, 0.78,
-                0.82, 0.88, 0.94, 1.00, 0.55, 0.39, 0.20, 0.01, 0.66, 0.54, 0.33, 0.02))
-filename = "ECO-dev-multi-panel.png"
-title_plot = "E. coli development dataset"
-} else if (organism == 'STM')
-{
-######### STM DEVELOPMENT DATASET ##########
-
-# STM-DEV-WITH-EFFECT-COMBINATION: Combination of strategies with effect in Salmonella evaluation dataset
-df <- data.frame(Panel=rep(c("Combination of strategies (effect)", "Separated strategies (effect)", "Combination of strategies (no effect)", "Separated strategies (no effect)"), each=12),
-                Measure=rep(c("Precision", "Recall", "F1-score"), each=4),
-                Strategy=c(rep(c("D", "D+V", "D+V+At", "D+V+At+Au"),3),rep(c("D", "V", "At", "Au"),3)),
-                Score=c(
-                0.78, 0.77, 0.76, 0.76, 0.33, 0.49, 0.54, 0.54, 0.47, 0.60, 0.63, 0.63,
-                0.78, 0.81, 0.70, 0.88, 0.33, 0.33, 0.10, 0.01, 0.47, 0.47, 0.18, 0.02,
-                0.84, 0.82, 0.81, 0.81, 0.47, 0.59, 0.65, 0.65, 0.60, 0.68, 0.72, 0.72,
-                0.84, 0.84, 0.77, 0.86, 0.47, 0.40, 0.17, 0.01, 0.60, 0.55, 0.27, 0.02))
-filename = "STM-dev-multi-panel.png"
-title_plot = "Salmonella evaluation dataset"
-}
-
-head(df)
-
-pa<-ggplot(df, aes(x=Strategy, y=Score, group=Measure)) +
-  geom_line(aes(color=Measure))+
-  geom_point(aes(color=Measure))+
-  scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
-  #scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
-  geom_text(aes(label = Score))+
-  labs(title=title_plot,x="Strategies", y = "Score")+
-  #theme_classic()+
-  theme(
-  legend.position="top",
-  # Centrar título: plot.title = element_text(hjust = 0.5),
-  axis.line = element_line(colour = "gray"),
-  panel.background = element_blank(),
-  panel.grid.major = element_blank(),
-  panel.grid.minor = element_blank(),
-  panel.border = element_blank(),
-  )+
-  facet_wrap(~Panel, scale="free")
-
-ggsave(filename)
-

+	Run1	Run2	Run3	Run4	Run5	Run6	Run7	Run8	Run9
+CV	0.9947569260999198	0.8753659172231524	0.871758460762884	0.8832373623657991	0.8736123942774514	0.8826022112505095	0.8772702934120828	0.8742694109779188	0.9916378145389343
+f1-score	1.000	0.796	0.762	0.797	0.770	0.802	0.788	0.809	0.995
+precision	1.000	0.834	0.795	0.837	0.777	0.815	0.803	0.856	1.000
+recall	1.000	0.769	0.749	0.767	0.778	0.800	0.783	0.772	0.991