Commit 913dff84 authored by Carine Rey's avatar Carine Rey
Browse files

update t_choices with the new hyps

parent 16858e78
......@@ -18,11 +18,13 @@ option_list = list(
make_option(c("--H0_NeG3" ) , type="character", default=NA, help="merged_results H0_NeG3)" , metavar="character"),
make_option(c("--H0_NeG4" ) , type="character", default=NA, help="merged_results H0_NeG4)" , metavar="character"),
make_option(c("--H0_NeG5" ) , type="character", default=NA, help="merged_results H0_NeG5)" , metavar="character"),
make_option(c("--H0_NeG6" ) , type="character", default=NA, help="merged_results H0_NeG6)" , metavar="character"),
make_option(c("--HaPC_NeG1" ) , type="character", default=NA, help="merged_results HaPC_NeG1" , metavar="character"),
make_option(c("--HaPC_NeG2" ) , type="character", default=NA, help="merged_results HaPC_NeG2" , metavar="character"),
make_option(c("--HaPC_NeG3" ) , type="character", default=NA, help="merged_results HaPC_NeG3" , metavar="character"),
make_option(c("--HaPC_NeG4" ) , type="character", default=NA, help="merged_results HaPC_NeG4" , metavar="character"),
make_option(c("--HaPC_NeG5" ) , type="character", default=NA, help="merged_results HaPC_NeG5" , metavar="character"),
make_option(c("--HaPC_NeG6" ) , type="character", default=NA, help="merged_results HaPC_NeG6" , metavar="character"),
make_option(c("--HaPC_NeG5_NeC_div2_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_NeC_div2_res" , metavar="character"),
make_option(c("--HaPC_NeG5_NeC_x2_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_NeC_x2_res" , metavar="character"),
make_option(c("--H0_NeG5_NeC_div2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_div2_res" , metavar="character"),
......@@ -37,6 +39,13 @@ option_list = list(
make_option(c("--HaPC_NeG1_NeC_4_res" ) , type="character", default=NA, help="merged_results HaPC_NeG1_NeC_4_res" , metavar="character"),
make_option(c("--H0_NeG1_NeC_4_res" ) , type="character", default=NA, help="merged_results H0_NeG1_NeC_4_res" , metavar="character"),
make_option(c("--HaPC_NeG4_NeC_6_res" ) , type="character", default=NA, help="merged_results HaPC_NeG4_NeC_6_res" , metavar="character"),
make_option(c("--H0_NeG4_NeC_6_res" ) , type="character", default=NA, help="merged_results H0_NeG4_NeC_6_res" , metavar="character"),
make_option(c("--HaPC_NeG2_NeC_4_res" ) , type="character", default=NA, help="merged_results HaPC_NeG2_NeC_4_res" , metavar="character"),
make_option(c("--H0_NeG2_NeC_4_res" ) , type="character", default=NA, help="merged_results H0_NeG2_NeC_4_res" , metavar="character"),
make_option(c("--HaPC_NeG4_NeC_2_res" ) , type="character", default=NA, help="merged_results HaPC_NeG4_NeC_2_res" , metavar="character"),
make_option(c("--H0_NeG4_NeC_2_res" ) , type="character", default=NA, help="merged_results H0_NeG4_NeC_2_res" , metavar="character"),
make_option(c("--H0_NeG5_indel_res" ) , type="character", default=NA, help="merged_results H0_NeG5_indel_res" , metavar="character"),
make_option(c("--HaPC_NeG5_indel_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_indel_res" , metavar="character"),
make_option(c("--HaPCOC" ) , type="character", default=NA, help="merged_results HaPCOC" , metavar="character"),
......@@ -86,11 +95,13 @@ df_H0_NeG2 = read_hyp(opt$H0_NeG2 )
df_H0_NeG3 = read_hyp(opt$H0_NeG3 )
df_H0_NeG4 = read_hyp(opt$H0_NeG4 )
df_H0_NeG5 = read_hyp(opt$H0_NeG5 )
df_H0_NeG6 = read_hyp(opt$H0_NeG6 )
df_HaPC_NeG1 = read_hyp(opt$HaPC_NeG1 )
df_HaPC_NeG2 = read_hyp(opt$HaPC_NeG2 )
df_HaPC_NeG3 = read_hyp(opt$HaPC_NeG3 )
df_HaPC_NeG4 = read_hyp(opt$HaPC_NeG4 )
df_HaPC_NeG5 = read_hyp(opt$HaPC_NeG5 )
df_HaPC_NeG6 = read_hyp(opt$HaPC_NeG6 )
df_HaPC_NeG5_NeC_div2 = read_hyp(opt$HaPC_NeG5_NeC_div2)
df_HaPC_NeG5_NeC_x2 = read_hyp(opt$HaPC_NeG5_NeC_x2 )
......@@ -107,6 +118,13 @@ df_H0_NeG4_NeC_1 = read_hyp(opt$H0_NeG4_NeC_1 )
df_HaPC_NeG1_NeC_4 = read_hyp(opt$HaPC_NeG1_NeC_4 )
df_H0_NeG1_NeC_4 = read_hyp(opt$H0_NeG1_NeC_4 )
df_HaPC_NeG4_NeC_6 = read_hyp(opt$HaPC_NeG4_NeC_6)
df_H0_NeG4_NeC_6 = read_hyp(opt$H0_NeG4_NeC_6 )
df_HaPC_NeG2_NeC_4 = read_hyp(opt$HaPC_NeG2_NeC_4 )
df_H0_NeG2_NeC_4 = read_hyp(opt$H0_NeG2_NeC_4 )
df_HaPC_NeG4_NeC_2 = read_hyp(opt$HaPC_NeG4_NeC_2 )
df_H0_NeG4_NeC_2 = read_hyp(opt$H0_NeG4_NeC_2 )
df_HaPC_NeG5_indel = read_hyp(opt$HaPC_NeG5_indel_res )
df_H0_NeG5_indel = read_hyp(opt$H0_NeG5_indel_res )
......@@ -142,6 +160,7 @@ df_d_H0HaPC_NeG2 = build_df_dist_couple(df_H0_NeG2, df_HaPC_NeG2, "H0/HaPC NeG
df_d_H0HaPC_NeG3 = build_df_dist_couple(df_H0_NeG3, df_HaPC_NeG3, "H0/HaPC NeG3")
df_d_H0HaPC_NeG4 = build_df_dist_couple(df_H0_NeG4, df_HaPC_NeG4, "H0/HaPC NeG4")
df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5")
df_d_H0HaPC_NeG6 = build_df_dist_couple(df_H0_NeG6, df_HaPC_NeG6, "H0/HaPC NeG6")
df_d_H0HaPC_NeG5_NeC_div2 = build_df_dist_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
df_d_H0HaPC_NeG5_NeC_x2 = build_df_dist_couple(df_H0_NeG5_NeC_x2, df_HaPC_NeG5_NeC_x2, "H0/HaPC NeG5_NeC_x2")
......@@ -152,6 +171,10 @@ df_d_H0HaPC_NeG1_NeC_5 = build_df_dist_couple(df_H0_NeG1_NeC_5, df_HaPC_NeG1_N
df_d_H0HaPC_NeG4_NeC_1 = build_df_dist_couple(df_H0_NeG4_NeC_1, df_HaPC_NeG4_NeC_1, "H0/HaPC NeG4_NeC_1")
df_d_H0HaPC_NeG1_NeC_4 = build_df_dist_couple(df_H0_NeG1_NeC_4, df_HaPC_NeG1_NeC_4, "H0/HaPC NeG1_NeC_4")
df_d_H0HaPC_NeG4_NeC_2 = build_df_dist_couple(df_H0_NeG4_NeC_2, df_HaPC_NeG4_NeC_2, "H0/HaPC NeG4_NeC_2")
df_d_H0HaPC_NeG2_NeC_4 = build_df_dist_couple(df_H0_NeG2_NeC_4, df_HaPC_NeG2_NeC_4, "H0/HaPC NeG2_NeC_4")
df_d_H0HaPC_NeG4_NeC_6 = build_df_dist_couple(df_H0_NeG4_NeC_6, df_HaPC_NeG4_NeC_6, "H0/HaPC NeG4_NeC_6")
df_d_H0HaPC_NeG5_indel = build_df_dist_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel")
df_d_H0H0_NeG1NeG1_NeC5 = build_df_dist_couple(df_H0_NeG1, df_H0_NeG1_NeC_5, "H0/H0 NeG1/NeG1_NeC_5")
......@@ -160,6 +183,10 @@ df_d_H0H0_NeG5NeG5_NeC1 = build_df_dist_couple(df_H0_NeG5, df_H0_NeG5_NeC_1, "
df_d_H0H0_NeG1NeG1_NeC4 = build_df_dist_couple(df_H0_NeG1, df_H0_NeG1_NeC_4, "H0/H0 NeG1/NeG1_NeC_4")
df_d_H0H0_NeG4NeG4_NeC1 = build_df_dist_couple(df_H0_NeG4, df_H0_NeG4_NeC_1, "H0/H0 NeG4/NeG4_NeC_1")
df_d_H0H0_NeG4NeG4_NeC_2 = build_df_dist_couple(df_H0_NeG4, df_H0_NeG4_NeC_2, "H0/H0 NeG4/NeG4_NeC_2")
df_d_H0H0_NeG2NeG2_NeC_4 = build_df_dist_couple(df_H0_NeG2, df_H0_NeG2_NeC_4, "H0/H0 NeG2/NeG2_NeC_4")
df_d_H0H0_NeG4NeG4_NeC_6 = build_df_dist_couple(df_H0_NeG4, df_H0_NeG4_NeC_6, "H0/H0 NeG4/NeG4_NeC_6")
df_d_H0_NeG1_HaPC_NeG1_NeC_4 = build_df_dist_couple(df_H0_NeG1, df_HaPC_NeG1_NeC_4, "H0 NeG1/HaPC NeG1_NeC_4")
df_d = rbind.data.frame(
......@@ -169,6 +196,7 @@ df_d = rbind.data.frame(
df_d_H0HaPC_NeG3,
df_d_H0HaPC_NeG4,
df_d_H0HaPC_NeG5,
df_d_H0HaPC_NeG6,
df_d_H0HaPC_NeG5_NeC_div2,
df_d_H0HaPC_NeG5_NeC_x2,
df_d_H0HaPC_NeG5_NeC_1,
......@@ -177,8 +205,14 @@ df_d = rbind.data.frame(
df_d_H0H0_NeG5NeG5_NeC1,
df_d_H0HaPC_NeG4_NeC_1,
df_d_H0HaPC_NeG1_NeC_4,
df_d_H0HaPC_NeG4_NeC_2
df_d_H0HaPC_NeG2_NeC_4
df_d_H0HaPC_NeG4_NeC_6
df_d_H0H0_NeG4NeG4_NeC1,
df_d_H0H0_NeG1NeG1_NeC4,
df_d_H0H0_NeG4NeG4_NeC_2,
df_d_H0H0_NeG2NeG2_NeC_4,
df_d_H0H0_NeG4NeG4_NeC_6,
df_d_H0_NeG1_HaPC_NeG1_NeC_4,
df_d_H0HaPC_NeG5_indel
)
......@@ -255,6 +289,7 @@ df_H0HaPC_NeG2 = build_df_couple(df_H0_NeG2, df_HaPC_NeG2, "H0/HaPC NeG2")
df_H0HaPC_NeG3 = build_df_couple(df_H0_NeG3, df_HaPC_NeG3, "H0/HaPC NeG3")
df_H0HaPC_NeG4 = build_df_couple(df_H0_NeG4, df_HaPC_NeG4, "H0/HaPC NeG4")
df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5")
df_H0HaPC_NeG6 = build_df_couple(df_H0_NeG5, df_HaPC_NeG6, "H0/HaPC NeG6")
df_H0HaPC_NeG5_NeC_div2 = build_df_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
......@@ -269,21 +304,37 @@ df_H0H0_NeG1NeG1_NeC_5 = build_df_couple(df_H0_NeG1, df_H0_NeG1_NeC_5, "H0/H0
df_H0HaPC_NeG4_NeC_1 = build_df_couple(df_H0_NeG4_NeC_1, df_HaPC_NeG4_NeC_1, "H0/HaPC NeG4_NeC_1")
df_H0HaPC_NeG1_NeC_4 = build_df_couple(df_H0_NeG1_NeC_4, df_HaPC_NeG1_NeC_4, "H0/HaPC NeG1_NeC_4")
df_H0HaPC_NeG4_NeC_2 = build_df_couple(df_H0_NeG4_NeC_2, df_HaPC_NeG4_NeC_2, "H0/HaPC NeG4_NeC_2")
df_H0HaPC_NeG2_NeC_4 = build_df_couple(df_H0_NeG2_NeC_4, df_HaPC_NeG2_NeC_4, "H0/HaPC NeG2_NeC_4")
df_H0HaPC_NeG4_NeC_6 = build_df_couple(df_H0_NeG4_NeC_6, df_HaPC_NeG4_NeC_6, "H0/HaPC NeG4_NeC_6")
df_H0H0_NeG4NeG4_NeC_1 = build_df_couple(df_H0_NeG4, df_H0_NeG4_NeC_1, "H0/H0 NeG4/NeG4_NeC_1")
df_H0H0_NeG1NeG1_NeC_4 = build_df_couple(df_H0_NeG1, df_H0_NeG1_NeC_4, "H0/H0 NeG1/NeG1_NeC_4")
df_H0H0_NeG4NeG4_NeC_2 = build_df_couple(df_H0_NeG4, df_H0_NeG4_NeC_2, "H0/H0 NeG4/NeG4_NeC_2")
df_H0H0_NeG2NeG2_NeC_4 = build_df_couple(df_H0_NeG2, df_H0_NeG2_NeC_4, "H0/H0 NeG2/NeG2_NeC_4")
df_H0H0_NeG4NeG4_NeC_6 = build_df_couple(df_H0_NeG4, df_H0_NeG4_NeC_6, "H0/H0 NeG4/NeG4_NeC_6")
df_H0_NeG1_HaPC_NeG1_NeC_4 = build_df_couple(df_H0_NeG1, df_HaPC_NeG1_NeC_4, "H0 NeG1/HaPC NeG1_NeC_4")
df_H0HaPC_NeG5_indel = build_df_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel")
df_l = list(df_H0HaPCOC_NeG1, df_H0HaPC_NeG1, df_H0HaPC_NeG2, df_H0HaPC_NeG3,
df_H0HaPC_NeG4, df_H0HaPC_NeG5, df_H0HaPC_NeG5_NeC_div2,
df_H0HaPC_NeG4, df_H0HaPC_NeG5,df_H0HaPC_NeG6, df_H0HaPC_NeG5_NeC_div2,
df_H0HaPC_NeG5_NeC_1,df_H0HaPC_NeG1_NeC_5,
df_H0H0_NeG5NeG5_NeC_1, df_H0H0_NeG1NeG1_NeC_5,
df_H0HaPC_NeG4_NeC_1,df_H0HaPC_NeG1_NeC_4,
df_H0HaPC_NeG4_NeC_2,
df_H0HaPC_NeG2_NeC_4,
df_H0HaPC_NeG4_NeC_6,
df_H0H0_NeG4NeG4_NeC_1, df_H0H0_NeG1NeG1_NeC_4,
df_H0_NeG1_HaPC_NeG1_NeC_4,
df_H0H0_NeG4NeG4_NeC_2,
df_H0H0_NeG2NeG2_NeC_4,
df_H0H0_NeG4NeG4_NeC_6,
df_H0HaPC_NeG5_NeC_x2,df_H0HaPC_NeG5_indel)
df_l = df_l[-which(sapply(df_l, is.null))]
......@@ -491,8 +542,8 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
)
print("plot recall_precision")
if (length(meths) <= 9 & all(c("H0 NeG1/HaPC NeG1_NeC_4","H0 NeG1/HaPC NeG1_NeC_4", "H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4","H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4", "H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4") %in% df_out$couple)) {
couple_i = c("H0 NeG1/HaPC NeG1_NeC_4", "H0 NeG1/HaPC NeG1_NeC_4", "H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG3","H0/HaPC NeG4","H0/HaPC NeG5","H0/H0 NeG5/NeG5_NeC_1","H0/H0 NeG1/NeG1_NeC_5", "H0/HaPC NeG5_NeC_1","H0/HaPC NeG1_NeC_5","H0/H0 NeG5/NeG4_NeC_1","H0/H0 NeG3/NeG1_NeC_4", "H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4")
if (length(meths) <= 9 & all(c("H0/HaPC NeG2","H0/HaPC NeG4","H0/HaPC NeG6","H0/H0 NeG4/NeG4_NeC_2","H0/H0 NeG4/NeG4_NeC_6","H0/H0 NeG2/NeG2_NeC_4","H0/HaPC NeG4_NeC_2","H0/HaPC NeG4_NeC_6","H0/HaPC NeG2_NeC_4","H0 NeG2/HaPC NeG2_NeC_4","H0 NeG4/HaPC NeG4_NeC_6") %in% df_out$couple)) {
couple_i = c("H0/HaPC NeG2","H0/HaPC NeG4","H0/HaPC NeG6","H0/H0 NeG4/NeG4_NeC_2","H0/H0 NeG4/NeG4_NeC_6","H0/H0 NeG2/NeG2_NeC_4","H0/HaPC NeG4_NeC_2","H0/HaPC NeG4_NeC_6","H0/HaPC NeG2_NeC_4","H0 NeG2/HaPC NeG2_NeC_4","H0 NeG4/HaPC NeG4_NeC_6")
plot = ggplot(subset(df_out, couple %in% couple_i), aes(x=sensitivity, y=precision98_02, col = methode))
plot = plot + theme_bw()
plot = plot + labs(x="Sensitivity (= Recall)", y="Precision (98/2)")
......@@ -573,11 +624,11 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
plot = plot + theme(axis.text.x = element_text(angle = 45, hjust = 1))
plot}
plot = plot_PR_c(c("H0/HaPC NeG","H0 NeG1/HaPC NeG1_NeC_4","H0/HaPC NeG2","H0/HaPC NeG4","H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4", "H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4"))
plot1 = plot_PR_c(c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4"))
plot2 = plot_PR_c(c("H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4","NULL"))
plot3 = plot_PR_c(c("H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4","NULL"))
plot4 = plot_PR_c(c("H0 NeG1/HaPC NeG1_NeC_4","NULL","NULL2"))
plot = plot_PR_c(c("H0/HaPC NeG2","H0/HaPC NeG4","H0/HaPC NeG6","H0/H0 NeG4/NeG4_NeC_2","H0/H0 NeG4/NeG4_NeC_6","H0/H0 NeG2/NeG2_NeC_4","H0/HaPC NeG4_NeC_2","H0/HaPC NeG4_NeC_6","H0/HaPC NeG2_NeC_4","H0 NeG2/HaPC NeG2_NeC_4","H0 NeG4/HaPC NeG4_NeC_6"))
plot1 = plot_PR_c(c("H0/HaPC NeG2","H0/HaPC NeG4","H0/HaPC NeG6"))
plot2 = plot_PR_c(c("H0/H0 NeG4/NeG4_NeC_2","H0/H0 NeG4/NeG4_NeC_6","H0/H0 NeG2/NeG2_NeC_4"))
plot3 = plot_PR_c(c("H0/HaPC NeG4_NeC_2","H0/HaPC NeG4_NeC_6","H0/HaPC NeG2_NeC_4"))
plot4 = plot_PR_c(c("H0 NeG2/HaPC NeG2_NeC_4","H0 NeG4/HaPC NeG4_NeC_6","NULL2"))
legend_PR = get_legend(plot + theme(legend.position="top",
legend.text = element_text(size=10),
......
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