Merge branch 'master' of http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions

+library(ggplot2)
+# Run1
+dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=4),
+Strategy=rep(c("OD", "Ph", "Technique", "Med", "Temp", "Vess", "Agit", "Phase", "Air", "Anti", "Strain", "Gtype", "Substrain", "Supp", "Gversion"),3),
+Score=c(
+1, 0.405, 0.577,
+1, 1, 1,
+0.88, 1, 0.936,
+0.852, 0.912, 0.881,
+0.818, 1, 0.9,
+0, 0, 0,
+0, 0, 0,
+1, 0.947, 0.973,
+0.92, 0.742, 0.821,
+1, 0.444, 0.615,
+1, 1, 1,
+0.905, 0.811, 0.856,
+0, 0, 0,
+0.883, 0.669, 0.762,
+0, 0, 0
+))
+# ECO-DEV-WITH-EFFECT-COMBINATION: Combination of strategies with effect in E. coli development dataset
+dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=4),
+Strategy=rep(c("Dev", "Dev+Vrb", "Dev+Vrb+Att", "Dev+Vrb+Att+Aut"),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))
+head(dfa)
+# Run1
+dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=15),
+Strategy=rep(c("OD", "Ph", "Technique", "Med", "Temp", "Vess", "Agit", "Phase", "Air", "Anti", "Strain", "Gtype", "Substrain", "Supp", "Gversion"),3),
+Score=c(
+1, 1, 0.88, 0.852, 0.818, 0, 0, 1, 0.92, 1, 1, 0.905, 0, 0.883, 0,
+0.405, 1, 1, 0.912, 1, 0, 0, 0.947, 0.742, 0.444, 1, 0.811, 0, 0.669, 0
+0.577, 1, 0.936, 0.881, 0.9, 0, 0, 0.973, 0.821, 0.615, 1, 0.856, 0, 0.762, 0
+))
+# Run1
+dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=15),
+Strategy=rep(c("OD", "Ph", "Technique", "Med", "Temp", "Vess", "Agit", "Phase", "Air", "Anti", "Strain", "Gtype", "Substrain", "Supp", "Gversion"),3),
+Score=c(
+1, 1, 0.88, 0.852, 0.818, 0, 0, 1, 0.92, 1, 1, 0.905, 0, 0.883, 0,
+0.405, 1, 1, 0.912, 1, 0, 0, 0.947, 0.742, 0.444, 1, 0.811, 0, 0.669, 0,
+0.577, 1, 0.936, 0.881, 0.9, 0, 0, 0.973, 0.821, 0.615, 1, 0.856, 0, 0.762, 0
+))
+head(dfa)
+pa<-ggplot(dfa, 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="Combination of strategies with effect in E. coli development dataset",x="Combination of strategies", y = "Score")+
+#labs(title="(a)",x="Combination of strategies", y = "Score")+
+theme_classic()
+pa
+title_plot = "Salmonella evaluation dataset"
+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(),
+)
+pa<-ggplot(dfa, 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="Combination of strategies with effect in E. coli development dataset",x="Combination of strategies", y = "Score")+
+#labs(title="(a)",x="Combination of strategies", 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")
+pa
+pa<-ggplot(dfa, 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="Prediction of best model (Run1)",x="Conditions", y = "Score")+
+#labs(title="(a)",x="Combination of strategies", 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
+# Run1
+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
+))
+head(dfa)
+pa<-ggplot(dfa, 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="Prediction of the best model (Run1)",x="Conditions", 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
+pa<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
+geom_line(aes(color=Measure, stat="identity"))+
+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="Prediction of the best model (Run1)",x="Conditions", 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<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
+geom_line(aes(color=Measure), stat="identity")+
+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="Prediction of the best model (Run1)",x="Conditions", 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

+# 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
+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
+                ))
+head(dfa)
+
+pa<-ggplot(dfa, 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="Prediction of the best model (Run1)",x="Conditions", 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)
+