Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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Estefani Gaytan Nunez
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1 -library(ggplot2)
2 -# Run1
3 -dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=4),
4 -Strategy=rep(c("OD", "Ph", "Technique", "Med", "Temp", "Vess", "Agit", "Phase", "Air", "Anti", "Strain", "Gtype", "Substrain", "Supp", "Gversion"),3),
5 -Score=c(
6 -1, 0.405, 0.577,
7 -1, 1, 1,
8 -0.88, 1, 0.936,
9 -0.852, 0.912, 0.881,
10 -0.818, 1, 0.9,
11 -0, 0, 0,
12 -0, 0, 0,
13 -1, 0.947, 0.973,
14 -0.92, 0.742, 0.821,
15 -1, 0.444, 0.615,
16 -1, 1, 1,
17 -0.905, 0.811, 0.856,
18 -0, 0, 0,
19 -0.883, 0.669, 0.762,
20 -0, 0, 0
21 -))
22 -# ECO-DEV-WITH-EFFECT-COMBINATION: Combination of strategies with effect in E. coli development dataset
23 -dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=4),
24 -Strategy=rep(c("Dev", "Dev+Vrb", "Dev+Vrb+Att", "Dev+Vrb+Att+Aut"),3),
25 -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))
26 -head(dfa)
27 -# Run1
28 -dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=15),
29 -Strategy=rep(c("OD", "Ph", "Technique", "Med", "Temp", "Vess", "Agit", "Phase", "Air", "Anti", "Strain", "Gtype", "Substrain", "Supp", "Gversion"),3),
30 -Score=c(
31 -1, 1, 0.88, 0.852, 0.818, 0, 0, 1, 0.92, 1, 1, 0.905, 0, 0.883, 0,
32 -0.405, 1, 1, 0.912, 1, 0, 0, 0.947, 0.742, 0.444, 1, 0.811, 0, 0.669, 0
33 -0.577, 1, 0.936, 0.881, 0.9, 0, 0, 0.973, 0.821, 0.615, 1, 0.856, 0, 0.762, 0
34 -))
35 -# Run1
36 -dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=15),
37 -Strategy=rep(c("OD", "Ph", "Technique", "Med", "Temp", "Vess", "Agit", "Phase", "Air", "Anti", "Strain", "Gtype", "Substrain", "Supp", "Gversion"),3),
38 -Score=c(
39 -1, 1, 0.88, 0.852, 0.818, 0, 0, 1, 0.92, 1, 1, 0.905, 0, 0.883, 0,
40 -0.405, 1, 1, 0.912, 1, 0, 0, 0.947, 0.742, 0.444, 1, 0.811, 0, 0.669, 0,
41 -0.577, 1, 0.936, 0.881, 0.9, 0, 0, 0.973, 0.821, 0.615, 1, 0.856, 0, 0.762, 0
42 -))
43 -head(dfa)
44 -pa<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
45 -geom_line(aes(color=Measure))+
46 -geom_point(aes(color=Measure))+
47 -scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
48 -#scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
49 -geom_text(aes(label = Score))+
50 -labs(title="Combination of strategies with effect in E. coli development dataset",x="Combination of strategies", y = "Score")+
51 -#labs(title="(a)",x="Combination of strategies", y = "Score")+
52 -theme_classic()
53 -pa
54 -title_plot = "Salmonella evaluation dataset"
55 -pa<-ggplot(df, aes(x=Strategy, y=Score, group=Measure)) +
56 -geom_line(aes(color=Measure))+
57 -geom_point(aes(color=Measure))+
58 -scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
59 -#scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
60 -geom_text(aes(label = Score))+
61 -labs(title=title_plot,x="Strategies", y = "Score")+
62 -#theme_classic()+
63 -theme(
64 -legend.position="top",
65 -# Centrar título: plot.title = element_text(hjust = 0.5),
66 -axis.line = element_line(colour = "gray"),
67 -panel.background = element_blank(),
68 -panel.grid.major = element_blank(),
69 -panel.grid.minor = element_blank(),
70 -panel.border = element_blank(),
71 -)
72 -pa<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
73 -geom_line(aes(color=Measure))+
74 -geom_point(aes(color=Measure))+
75 -scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
76 -#scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
77 -geom_text(aes(label = Score))+
78 -labs(title="Combination of strategies with effect in E. coli development dataset",x="Combination of strategies", y = "Score")+
79 -#labs(title="(a)",x="Combination of strategies", y = "Score")+
80 -theme(
81 -legend.position="top",
82 -# Centrar título: plot.title = element_text(hjust = 0.5),
83 -axis.line = element_line(colour = "gray"),
84 -panel.background = element_blank(),
85 -panel.grid.major = element_blank(),
86 -panel.grid.minor = element_blank(),
87 -panel.border = element_blank()
88 -)
89 -pa
90 -ggsave(".png")
91 -pa
92 -pa<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
93 -geom_line(aes(color=Measure))+
94 -geom_point(aes(color=Measure))+
95 -scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
96 -#scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
97 -geom_text(aes(label = Score))+
98 -labs(title="Prediction of best model (Run1)",x="Conditions", y = "Score")+
99 -#labs(title="(a)",x="Combination of strategies", y = "Score")+
100 -theme(
101 -legend.position="top",
102 -# Centrar título: plot.title = element_text(hjust = 0.5),
103 -axis.line = element_line(colour = "gray"),
104 -panel.background = element_blank(),
105 -panel.grid.major = element_blank(),
106 -panel.grid.minor = element_blank(),
107 -panel.border = element_blank()
108 -)
109 -pa
110 -# Run1
111 -dfa <- data.frame(Measure=rep(c("Precision", "Recall", "F1-score"), each=15),
112 -Strategy=rep(c(
113 -"Agit",
114 -"Gversion",
115 -"Substrain",
116 -"Vess",
117 -"OD",
118 -"Anti",
119 -"Supp",
120 -"Air",
121 -"Gtype",
122 -"Med",
123 -"Temp",
124 -"Technique",
125 -"Phase",
126 -"pH",
127 -"Strain"
128 -),3),
129 -Score=c(
130 -0,
131 -0,
132 -0,
133 -0,
134 -1,
135 -1,
136 -0.883,
137 -0.92,
138 -0.905,
139 -0.852,
140 -0.818,
141 -0.88,
142 -1,
143 -1,
144 -1,
145 -0,
146 -0,
147 -0,
148 -0,
149 -0.405,
150 -0.444,
151 -0.669,
152 -0.742,
153 -0.811,
154 -0.912,
155 -1,
156 -1,
157 -0.947,
158 -1,
159 -1,
160 -0,
161 -0,
162 -0,
163 -0,
164 -0.577,
165 -0.615,
166 -0.762,
167 -0.821,
168 -0.856,
169 -0.881,
170 -0.9,
171 -0.936,
172 -0.973,
173 -1,
174 -1
175 -))
176 -head(dfa)
177 -pa<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
178 -geom_line(aes(color=Measure))+
179 -geom_point(aes(color=Measure))+
180 -scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
181 -#scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
182 -geom_text(aes(label = Score))+
183 -labs(title="Prediction of the best model (Run1)",x="Conditions", y = "Score")+
184 -theme(
185 -legend.position="top",
186 -# Centrar título: plot.title = element_text(hjust = 0.5),
187 -axis.line = element_line(colour = "gray"),
188 -panel.background = element_blank(),
189 -panel.grid.major = element_blank(),
190 -panel.grid.minor = element_blank(),
191 -panel.border = element_blank()
192 -)
193 -pa
194 -pa<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
195 -geom_line(aes(color=Measure, stat="identity"))+
196 -geom_point(aes(color=Measure))+
197 -scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
198 -#scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
199 -geom_text(aes(label = Score))+
200 -labs(title="Prediction of the best model (Run1)",x="Conditions", y = "Score")+
201 -theme(
202 -legend.position="top",
203 -# Centrar título: plot.title = element_text(hjust = 0.5),
204 -axis.line = element_line(colour = "gray"),
205 -panel.background = element_blank(),
206 -panel.grid.major = element_blank(),
207 -panel.grid.minor = element_blank(),
208 -panel.border = element_blank()
209 -)
210 -pa<-ggplot(dfa, aes(x=Strategy, y=Score, group=Measure)) +
211 -geom_line(aes(color=Measure), stat="identity")+
212 -geom_point(aes(color=Measure))+
213 -scale_color_manual(values=c("#999999", "#E69F00", "#56B4E9"))+
214 -#scale_color_manual(values=c("#e6194b", "#3cb44b", "#0082c8"))+
215 -geom_text(aes(label = Score))+
216 -labs(title="Prediction of the best model (Run1)",x="Conditions", y = "Score")+
217 -theme(
218 -legend.position="top",
219 -# Centrar título: plot.title = element_text(hjust = 0.5),
220 -axis.line = element_line(colour = "gray"),
221 -panel.background = element_blank(),
222 -panel.grid.major = element_blank(),
223 -panel.grid.minor = element_blank(),
224 -panel.border = element_blank()
225 -)
226 -pa