Commit 7cfa4b5b authored by Carine Rey's avatar Carine Rey
Browse files

prep figures

parent 1a767716
...@@ -92,7 +92,7 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n ...@@ -92,7 +92,7 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
[Fixed 4.] @ if preview then [Variable (8., 1.)] else [Fixed 4.] @ if preview then [Variable (8., 1.)] else
[Fixed 1.; Fixed 8.; (* 4->8, 8->4, 8, 16, 1->8 and 16->1 are new ; it means 6*2*2 tasks on cyp/C4A *) [Fixed 1.; Fixed 8.; (* 4->8, 8->4, 8, 16, 1->8 and 16->1 are new ; it means 6*2*2 tasks on cyp/C4A *)
Variable (1., 4.); Variable (4., 1.); Variable (1., 4.); Variable (4., 1.);
Variable (4., 8.); Variable (8., 1.); Variable (4., 8.);
] ]
in in
let models = h0_hapc_forall nes_list in let models = h0_hapc_forall nes_list in
......
...@@ -681,9 +681,9 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -681,9 +681,9 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
print("plot recall_precision") print("plot recall_precision")
couple_plot1 = c("H0/HaPC NeG1","H0/HaPC NeG4","H0/HaPC NeG8") couple_plot1 = c("H0/HaPC NeG1","H0/HaPC NeG4","H0/HaPC NeG8")
couple_plot2 = c("H0/H0 NeG1/NeG1_NeC_4","H0/H0 NeG4/NeG4_NeC_8","H0/H0 NeG8/NeG8_NeC_1") couple_plot2 = c("H0/H0 NeG1/NeG1_NeC_4","H0/H0 NeG4/NeG4_NeC_8","H0/H0 NeG4/NeG4_NeC_1")
couple_plot3 = c("H0/HaPC NeG1_NeC_4", "H0/HaPC NeG4_NeC_8","H0/HaPC NeG8_NeC_1") couple_plot3 = c("H0/HaPC NeG1_NeC_4", "H0/HaPC NeG4_NeC_8","H0/HaPC NeG4_NeC_1")
couple_plot4 = c("H0 NeG1/HaPC NeG1_NeC_4","H0 NeG4/HaPC NeG4_NeC_8","H0 NeG8/HaPC NeG8_NeC_1") couple_plot4 = c("H0 NeG1/HaPC NeG1_NeC_4","H0 NeG4/HaPC NeG4_NeC_8","H0 NeG4/HaPC NeG4_NeC_1")
couple_i = c(couple_plot1,couple_plot2,couple_plot3,couple_plot4) couple_i = c(couple_plot1,couple_plot2,couple_plot3,couple_plot4)
...@@ -737,7 +737,6 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -737,7 +737,6 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot_PR_c = function(couple_l) { plot_PR_c = function(couple_l) {
if (sum(couple_l%in%df_out$couple) > 0) { if (sum(couple_l%in%df_out$couple) > 0) {
print ("PAS OK")
tmp_df = subset(df_out,couple%in%couple_l) tmp_df = subset(df_out,couple%in%couple_l)
tmp_df$couple = factor( tmp_df$couple, levels=c(levels( tmp_df$couple),"to_be_rm","to_be_rm2","to_be_rm3","to_be_rm4")) tmp_df$couple = factor( tmp_df$couple, levels=c(levels( tmp_df$couple),"to_be_rm","to_be_rm2","to_be_rm3","to_be_rm4"))
...@@ -765,11 +764,12 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -765,11 +764,12 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
from_c= c(couple_plot1,couple_plot2,couple_plot3,couple_plot4) from_c= c(couple_plot1,couple_plot2,couple_plot3,couple_plot4)
couple_plot1_to = c("PC NeS 1","PC NeS 4","PC NeS 8") couple_plot1_to = c("PC NeS 1","PC NeS 4","PC NeS 8")
couple_plot2_to = c("CCSE NeSA1 NeSC 4","CCSE NeSA4 NeSC 8","CCSE NeSA8 NeSC 1") couple_plot2_to = c("CCSE NeSA1 NeSC 4","CCSE NeSA4 NeSC 8","CCSE NeSA8 NeSC 1")
couple_plot3_to = c("PC & GCSE NeSA1 NeSC 4","PC & GCSE NeSA4 NeSC 8","PC & GCSE NeSA8 NeSC 1") couple_plot3_to = c("PC & GCSE NeSA1 NeSC 4","PC & GCSE NeSA4 NeSC 8","PC & GCSE NeSA4 NeSC 1")
couple_plot4_to = c("PC & CCSE NeSA1 NeSC 4","PC & CCSE NeSA4 NeSC 8","PC & CCSE NeSA8 NeSC 1") couple_plot4_to = c("PC & CCSE NeSA1 NeSC 4","PC & CCSE NeSA4 NeSC 8","PC & CCSE NeSA4 NeSC 1")
to_c= c(couple_plot1_to,couple_plot2_to,couple_plot3_to,couple_plot4_to) to_c= c(couple_plot1_to,couple_plot2_to,couple_plot3_to,couple_plot4_to)
tmp_df$coupleF = mapvalues(tmp_df$couple, from=from_c, to=to_c) tmp_df$coupleF = mapvalues(tmp_df$couple, from=from_c, to=to_c)
tmp_df$coupleF = factor(tmp_df$coupleF, levels =unique(c(couple_plot1_to,couple_plot2_to,couple_plot4_to,couple_plot3_to))) tmp_df$coupleF = factor(tmp_df$coupleF, levels =unique(c(couple_plot1_to,couple_plot2_to,couple_plot4_to,couple_plot3_to)))
tmp_df$coupleF = factor( tmp_df$coupleF, levels=c(levels( tmp_df$coupleF),"to_be_rm","to_be_rm2","to_be_rm3","to_be_rm4"))
plot = ggplot(tmp_df, aes(x=sensitivity, y=precision98_02, col = methode)) plot = ggplot(tmp_df, aes(x=sensitivity, y=precision98_02, col = methode))
plot = plot + theme_bw() plot = plot + theme_bw()
...@@ -820,9 +820,9 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -820,9 +820,9 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
couple_simuA = c("H0/HaPC NeG1","H0/HaPC NeG4","H0/HaPC NeG8") couple_simuA = c("H0/HaPC NeG1","H0/HaPC NeG4","H0/HaPC NeG8")
couple_simuB = c("H0/H0 NeG1/NeG1_NeC_4","H0/H0 NeG4/NeG4_NeC_8","H0/H0 NeG8/NeG8_NeC_1") couple_simuB = c("H0/H0 NeG1/NeG1_NeC_4","H0/H0 NeG4/NeG4_NeC_8","H0/H0 NeG4/NeG4_NeC_1")
couple_simuC = c("H0/HaPC NeG1","H0/HaPC NeG8_NeC_1","H0/HaPC NeG4","H0/HaPC NeG1_NeC_4","H0/HaPC NeG8", "H0/HaPC NeG4_NeC_8") couple_simuC = c("H0/HaPC NeG1","H0/HaPC NeG4_NeC_1","H0/HaPC NeG4","H0/HaPC NeG1_NeC_4","H0/HaPC NeG8", "H0/HaPC NeG4_NeC_8")
couple_simuD = c("H0/HaPC NeG1","H0/HaPC NeG4","H0/HaPC NeG8", "H0 NeG1/HaPC NeG1_NeC_4","H0 NeG4/HaPC NeG4_NeC_8","H0 NeG8/HaPC NeG8_NeC_1") couple_simuD = c("H0/HaPC NeG1","H0/HaPC NeG4","H0/HaPC NeG8", "H0 NeG1/HaPC NeG1_NeC_4","H0 NeG4/HaPC NeG4_NeC_8","H0 NeG4/HaPC NeG4_NeC_1")
tmp_df$group[tmp_df$couple%in%couple_simuA] = "PC" tmp_df$group[tmp_df$couple%in%couple_simuA] = "PC"
...@@ -849,12 +849,12 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -849,12 +849,12 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
from_c= c(couple_plot1,couple_plot2,couple_plot3,couple_plot4) from_c= c(couple_plot1,couple_plot2,couple_plot3,couple_plot4)
couple_plot1_to = c("NeS 1","NeS 4","NeS 8") couple_plot1_to = c("NeS 1","NeS 4","NeS 8")
couple_plot2_to = c("NeSA 1\nNeSC 4","NeSA 4\nNeSC 8","NeSA 8\nNeSC 1") couple_plot2_to = c("NeSA 1\nNeSC 4","NeSA 4\nNeSC 8","NeSA 4\nNeSC 1")
couple_plot3_to = c("NeSA 1\nNeSC 4","NeSA 4\nNeSC 8","NeSA 8\nNeSC 1") couple_plot3_to = c("NeSA 1\nNeSC 4","NeSA 4\nNeSC 8","NeSA 4\nNeSC 1")
couple_plot4_to = c("NeSA 1\nNeSC 4","NeSA 4\nNeSC 8","NeSA 8\nNeSC 1") couple_plot4_to = c("NeSA 1\nNeSC 4","NeSA 4\nNeSC 8","NeSA 4\nNeSC 1")
to_c= c(couple_plot1_to,couple_plot2_to,couple_plot3_to,couple_plot4_to) to_c= c(couple_plot1_to,couple_plot2_to,couple_plot3_to,couple_plot4_to)
tmp_df$coupleX = mapvalues(tmp_df$couple, from=from_c, to=to_c) tmp_df$coupleX = mapvalues(tmp_df$couple, from=from_c, to=to_c)
tmp_df$coupleX = factor(tmp_df$coupleX, levels =c("NeS 1","NeSA 8\nNeSC 1","NeS 4","NeSA 1\nNeSC 4","NeS 8","NeSA 4\nNeSC 8")) tmp_df$coupleX = factor(tmp_df$coupleX, levels =c("NeS 1","NeSA 4\nNeSC 1","NeS 4","NeSA 1\nNeSC 4","NeS 8","NeSA 4\nNeSC 8"))
from_m=c("PCOC","Mutinomial_1MinusLRT", "Msd_0.05_1MinusP", "Identical_LG08", "Tdg09_1MinusLRT","Topological_LG08","Diffsel_mean") from_m=c("PCOC","Mutinomial_1MinusLRT", "Msd_0.05_1MinusP", "Identical_LG08", "Tdg09_1MinusLRT","Topological_LG08","Diffsel_mean")
to_m=c("PCOC","Mutinomial", "msd", "Identical", "TDG09","Topological","diffsel") to_m=c("PCOC","Mutinomial", "msd", "Identical", "TDG09","Topological","diffsel")
...@@ -866,7 +866,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -866,7 +866,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot = plot + labs(x="", y="AUC") plot = plot + labs(x="", y="AUC")
plot = plot + theme(legend.position="top") plot = plot + theme(legend.position="top")
plot = plot + ylim(c(0,1)) plot = plot + ylim(c(0,1))
plot = plot + guides(fill=FALSE) #plot = plot + guides(fill=FALSE)
plot = plot + scale_color_manual(values=colors2) plot = plot + scale_color_manual(values=colors2)
plot = plot + scale_fill_manual(values=colors2) plot = plot + scale_fill_manual(values=colors2)
#plot = plot + geom_point(size=1, alpha=alpha) #plot = plot + geom_point(size=1, alpha=alpha)
...@@ -911,7 +911,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -911,7 +911,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot = plot + labs(x="", y="Recall at 90% of precision") plot = plot + labs(x="", y="Recall at 90% of precision")
plot = plot + theme(legend.position="top") plot = plot + theme(legend.position="top")
plot = plot + ylim(c(0,1)) plot = plot + ylim(c(0,1))
plot = plot + guides(fill=FALSE) #plot = plot + guides(fill=FALSE)
plot = plot + scale_color_manual(values=colors2) plot = plot + scale_color_manual(values=colors2)
#plot = plot + geom_point(size=1, alpha=alpha) #plot = plot + geom_point(size=1, alpha=alpha)
plot = plot + geom_point(na.rm=TRUE, position=position_dodge(width=0.5),size=1.5,alpha=1) plot = plot + geom_point(na.rm=TRUE, position=position_dodge(width=0.5),size=1.5,alpha=1)
...@@ -922,7 +922,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL ...@@ -922,7 +922,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot = plot_PR_c(couple_i) plot = plot_PR_c(couple_i)
plot1 = plot_PR_c(couple_plot1) plot1 = plot_PR_c(couple_plot1)
plot1 = plot_PR_c(c("H0/HaPC NeG4","NULL2","NULL")) plot1 = plot_PR_c(c("NULL","H0/HaPC NeG4","NULL2"))
plot2 = plot_PR_c(couple_plot2) plot2 = plot_PR_c(couple_plot2)
plot3 = plot_PR_c(couple_plot3) plot3 = plot_PR_c(couple_plot3)
plot4 = plot_PR_c(couple_plot4) plot4 = plot_PR_c(couple_plot4)
......
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