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Commit d1645dc4 authored by Carine Rey's avatar Carine Rey
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update final figure

parent a498fd88
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Showing with 36 additions and 15 deletions
lib/post_analyses.ml
View file @ d1645dc4
......@@ -73,8 +73,8 @@ let build_cmd_t_choices (opt_name : string) mr_option =
| None -> []
let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~h0_NeG1_mr ~h0_NeG2_mr ~h0_NeG3_mr ~h0_NeG4_mr ~h0_NeG5_mr ~h0_NeG6_mr
~haPC_NeG1_mr ~haPC_NeG2_mr ~haPC_NeG3_mr ~haPC_NeG4_mr ~haPC_NeG5_mr ~haPC_NeG6_mr
~h0_NeG1_mr ~h0_NeG2_mr ~h0_NeG3_mr ~h0_NeG4_mr ~h0_NeG5_mr ~h0_NeG6_mr ~h0_NeG8_mr
~haPC_NeG1_mr ~haPC_NeG2_mr ~haPC_NeG3_mr ~haPC_NeG4_mr ~haPC_NeG5_mr ~haPC_NeG6_mr ~haPC_NeG8_mr
~haPC_NeG5_NeC_div2_mr
~haPC_NeG5_NeC_x2_mr
~h0_NeG5_NeC_div2_mr
......@@ -107,12 +107,14 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
("--H0_NeG4" , h0_NeG4_mr );
("--H0_NeG5" , h0_NeG5_mr );
("--H0_NeG6" , h0_NeG6_mr );
("--H0_NeG8" , h0_NeG8_mr );
("--HaPC_NeG1" , haPC_NeG1_mr );
("--HaPC_NeG2" , haPC_NeG2_mr );
("--HaPC_NeG3" , haPC_NeG3_mr );
("--HaPC_NeG4" , haPC_NeG4_mr );
("--HaPC_NeG5" , haPC_NeG5_mr );
("--HaPC_NeG6" , haPC_NeG6_mr );
("--HaPC_NeG8" , haPC_NeG8_mr );
("--HaPC_NeG5_NeC_div2_res" , haPC_NeG5_NeC_div2_mr );
("--HaPC_NeG5_NeC_x2_res" , haPC_NeG5_NeC_x2_mr );
("--H0_NeG5_NeC_div2_res" , h0_NeG5_NeC_div2_mr );
......@@ -230,12 +232,14 @@ type res_all_hyp = {
h0_NeG4_res : dataset_res option ;
h0_NeG5_res : dataset_res option ;
h0_NeG6_res : dataset_res option ;
h0_NeG8_res : dataset_res option ;
haPC_NeG1_res : dataset_res option ;
haPC_NeG2_res : dataset_res option ;
haPC_NeG3_res : dataset_res option ;
haPC_NeG4_res : dataset_res option ;
haPC_NeG5_res : dataset_res option ;
haPC_NeG6_res : dataset_res option ;
haPC_NeG8_res : dataset_res option ;
haPC_NeG5_NeC_div2_res : dataset_res option ;
haPC_NeG5_NeC_x2_res : dataset_res option ;
h0_NeG5_NeC_div2_res : dataset_res option ;
......@@ -265,12 +269,12 @@ type res_all_hyp = {
}
let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res; h0_NeG6_res;
h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res; h0_NeG6_res; h0_NeG8_res;
haPC_NeG1_res;
haPC_NeG2_res;
haPC_NeG3_res;
haPC_NeG4_res;
haPC_NeG5_res; haPC_NeG6_res;
haPC_NeG5_res; haPC_NeG6_res; haPC_NeG8_res;
haPC_NeG5_NeC_div2_res;
haPC_NeG5_NeC_x2_res ;
h0_NeG5_NeC_div2_res ;
......@@ -303,12 +307,14 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
let h0_NeG4_mr = get_merged_results_opt h0_NeG4_res in
let h0_NeG5_mr = get_merged_results_opt h0_NeG5_res in
let h0_NeG6_mr = get_merged_results_opt h0_NeG6_res in
let h0_NeG8_mr = get_merged_results_opt h0_NeG8_res in
let haPC_NeG1_mr = get_merged_results_opt haPC_NeG1_res in
let haPC_NeG2_mr = get_merged_results_opt haPC_NeG2_res in
let haPC_NeG3_mr = get_merged_results_opt haPC_NeG3_res in
let haPC_NeG4_mr = get_merged_results_opt haPC_NeG4_res in
let haPC_NeG5_mr = get_merged_results_opt haPC_NeG5_res in
let haPC_NeG6_mr = get_merged_results_opt haPC_NeG6_res in
let haPC_NeG8_mr = get_merged_results_opt haPC_NeG8_res in
let haPC_NeG5_NeC_div2_mr = get_merged_results_opt haPC_NeG5_NeC_div2_res in
let haPC_NeG5_NeC_x2_mr = get_merged_results_opt haPC_NeG5_NeC_x2_res in
......@@ -344,12 +350,14 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
~h0_NeG4_mr
~h0_NeG5_mr
~h0_NeG6_mr
~h0_NeG8_mr
~haPC_NeG1_mr
~haPC_NeG2_mr
~haPC_NeG3_mr
~haPC_NeG4_mr
~haPC_NeG5_mr
~haPC_NeG6_mr
~haPC_NeG8_mr
~haPC_NeG5_NeC_div2_mr
~haPC_NeG5_NeC_x2_mr
~h0_NeG5_NeC_div2_mr
......@@ -385,12 +393,14 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let h0_NeG4_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG4" ) in
let h0_NeG5_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5" ) in
let h0_NeG6_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG6" ) in
let h0_NeG8_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG8" ) in
let haPC_NeG1_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG1" ) in
let haPC_NeG2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG2" ) in
let haPC_NeG3_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG3" ) in
let haPC_NeG4_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG4" ) in
let haPC_NeG5_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5" ) in
let haPC_NeG6_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG6" ) in
let haPC_NeG8_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG8" ) in
let haPC_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_div2" ) in
let haPC_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_x2" ) in
......@@ -423,8 +433,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
match (h0_NeG4_res) with
| ( Some h0_NeG4) ->
let t_choices_dir = make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res; h0_NeG6_res;
haPC_NeG1_res; haPC_NeG2_res;haPC_NeG3_res; haPC_NeG4_res; haPC_NeG5_res; haPC_NeG6_res;
h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res; h0_NeG6_res; h0_NeG8_res;
haPC_NeG1_res; haPC_NeG2_res;haPC_NeG3_res; haPC_NeG4_res; haPC_NeG5_res; haPC_NeG6_res; haPC_NeG8_res;
haPC_NeG5_NeC_div2_res; haPC_NeG5_NeC_x2_res; h0_NeG5_NeC_div2_res; h0_NeG5_NeC_x2_res;
haPC_NeG4_NeC_1_res; haPC_NeG4_NeC_8_res; haPC_NeG1_NeC_4_res; h0_NeG1_NeC_4_res; h0_NeG4_NeC_1_res; h0_NeG4_NeC_8_res;
haPC_NeG5_NeC_1_res; haPC_NeG1_NeC_5_res; h0_NeG1_NeC_5_res; h0_NeG5_NeC_1_res;
......
lib/scripts/calc_t_per_meth.R
View file @ d1645dc4
......@@ -19,12 +19,14 @@ option_list = list(
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("--H0_NeG8" ) , type="character", default=NA, help="merged_results H0_NeG8)" , 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_NeG8" ) , type="character", default=NA, help="merged_results HaPC_NeG8" , 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"),
......@@ -93,12 +95,14 @@ 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_H0_NeG8 = read_hyp(opt$H0_NeG8 )
df_HaPC_NeG1 = read_hyp(opt$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$HaPC_NeG6 )
df_HaPC_NeG8 = read_hyp(opt$HaPC_NeG8 )
df_HaPC_NeG5_NeC_div2 = read_hyp(opt$HaPC_NeG5_NeC_div2)
df_HaPC_NeG5_NeC_x2 = read_hyp(opt$HaPC_NeG5_NeC_x2 )
......@@ -157,6 +161,7 @@ df_d_H0HaPC_NeG3 = build_df_dist_couple(df_H0_NeG3, df_HaPC_NeG3, "H0/HaPC NeG
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_NeG8 = build_df_dist_couple(df_H0_NeG8, df_HaPC_NeG8, "H0/HaPC NeG8")
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")
......@@ -186,6 +191,7 @@ df_d_H0H0_NeG2NeG2_NeC_4 = build_df_dist_couple(df_H0_NeG2, df_H0_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_H0_NeG4_HaPC_NeG4_NeC_1 = build_df_dist_couple(df_H0_NeG4, df_HaPC_NeG4_NeC_1, "H0 NeG4/HaPC NeG4_NeC_1")
df_d_H0_NeG2_HaPC_NeG2_NeC_4 = build_df_dist_couple(df_H0_NeG2, df_HaPC_NeG2_NeC_4, "H0 NeG2/HaPC NeG2_NeC_4")
df_d_H0_NeG4_HaPC_NeG4_NeC_6 = build_df_dist_couple(df_H0_NeG4, df_HaPC_NeG4_NeC_6, "H0 NeG4/HaPC NeG4_NeC_6")
df_d_H0_NeG4_HaPC_NeG4_NeC_8 = build_df_dist_couple(df_H0_NeG4, df_HaPC_NeG4_NeC_8, "H0 NeG4/HaPC NeG4_NeC_8")
......@@ -198,6 +204,7 @@ df_d = rbind.data.frame(
df_d_H0HaPC_NeG4,
df_d_H0HaPC_NeG5,
df_d_H0HaPC_NeG6,
df_d_H0HaPC_NeG8,
df_d_H0HaPC_NeG5_NeC_div2,
df_d_H0HaPC_NeG5_NeC_x2,
df_d_H0HaPC_NeG5_NeC_1,
......@@ -217,6 +224,7 @@ df_d = rbind.data.frame(
df_d_H0H0_NeG2NeG2_NeC_4,
df_d_H0H0_NeG4NeG4_NeC_6,
df_d_H0_NeG1_HaPC_NeG1_NeC_4,
df_d_H0_NeG4_HaPC_NeG4_NeC_1,
df_d_H0_NeG2_HaPC_NeG2_NeC_4,
df_d_H0HaPC_NeG5_indel,
df_d_H0_NeG4_HaPC_NeG4_NeC_6,
......@@ -296,6 +304,7 @@ 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_NeG6, df_HaPC_NeG6, "H0/HaPC NeG6")
df_H0HaPC_NeG8 = build_df_couple(df_H0_NeG8, df_HaPC_NeG8, "H0/HaPC NeG8")
df_H0HaPC_NeG5_NeC_div2 = build_df_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
......@@ -326,6 +335,7 @@ df_H0H0_NeG4NeG4_NeC_6 = build_df_couple(df_H0_NeG4, df_H0_NeG4_NeC_6, "H0/H0
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_H0_NeG4_HaPC_NeG4_NeC_1 = build_df_couple(df_H0_NeG4, df_HaPC_NeG4_NeC_1, "H0 NeG4/HaPC NeG4_NeC_1")
df_H0_NeG2_HaPC_NeG2_NeC_4 = build_df_couple(df_H0_NeG2, df_HaPC_NeG2_NeC_4, "H0 NeG2/HaPC NeG2_NeC_4")
df_H0_NeG4_HaPC_NeG4_NeC_6 = build_df_couple(df_H0_NeG4, df_HaPC_NeG4_NeC_6, "H0 NeG4/HaPC NeG4_NeC_6")
df_H0_NeG4_HaPC_NeG4_NeC_8 = build_df_couple(df_H0_NeG4, df_HaPC_NeG4_NeC_8, "H0 NeG4/HaPC NeG4_NeC_8")
......@@ -334,7 +344,7 @@ df_H0HaPC_NeG5_indel = build_df_couple(df_H0_NeG5_indel, df_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_NeG6, df_H0HaPC_NeG5_NeC_div2,
df_H0HaPC_NeG4, df_H0HaPC_NeG5,df_H0HaPC_NeG6, df_H0HaPC_NeG8, 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,
......@@ -348,6 +358,7 @@ df_l = list(df_H0HaPCOC_NeG1, df_H0HaPC_NeG1, df_H0HaPC_NeG2, df_H0HaPC_NeG3,
df_H0_NeG2_HaPC_NeG2_NeC_4,
df_H0H0_NeG4NeG4_NeC_6,
df_H0_NeG4_HaPC_NeG4_NeC_6,
df_H0_NeG4_HaPC_NeG4_NeC_1,
df_H0HaPC_NeG4_NeC_8, df_H0_NeG4_HaPC_NeG4_NeC_8,df_H0H0_NeG4NeG4_NeC_8,
df_H0HaPC_NeG5_NeC_x2,df_H0HaPC_NeG5_indel)
......@@ -556,10 +567,10 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
)
print("plot recall_precision")
couple_plot1 = c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4","H0/HaPC NeG6","NULL","NULL2")
couple_plot2 = c("H0/H0 NeG4/NeG4_NeC_2","H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG4/NeG4_NeC_6","H0/H0 NeG4/NeG4_NeC_8","H0/H0 NeG2/NeG2_NeC_4","H0/H0 NeG1/NeG1_NeC_4")
couple_plot3 = c("H0/HaPC NeG4_NeC_2","H0/HaPC NeG4_NeC_6","H0/HaPC NeG2_NeC_4","H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4","H0/HaPC NeG4_NeC_8")
couple_plot4 = c("H0 NeG1/HaPC NeG1_NeC_4","H0 NeG2/HaPC NeG2_NeC_4","H0 NeG4/HaPC NeG4_NeC_6","H0 NeG4/HaPC NeG4_NeC_8","NULL","NULL2")
couple_plot1 = c("H0/HaPC NeG1","H0/HaPC NeG4","H0/HaPC NeG8")
couple_plot2 = c("H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG4/NeG4_NeC_8","H0/H0 NeG1/NeG1_NeC_4")
couple_plot3 = c("H0/HaPC NeG4_NeC_8","H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4")
couple_plot4 = c("H0 NeG1/HaPC NeG1_NeC_4","H0 NeG4/HaPC NeG4_NeC_1","H0 NeG4/HaPC NeG4_NeC_8")
couple_i = c(couple_plot1,couple_plot2,couple_plot3,couple_plot4)
......@@ -650,8 +661,8 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
df_auc_label$methode = mapvalues(df_auc_label$methode, from=from_m, to=to_m)
df_auc_label$label = substr(as.character(df_auc_label$auc2), 1,5)
df_auc_leg = data.frame(couple = unique(tmp_df$couple), x = 0.9, y = 0.8, label = "AUC ")
plot = plot + geom_label(data=df_auc_label, aes(x=0.9, y=y, label=label, col=methode))
plot = plot + geom_label(data=df_auc_leg, aes(x=x, y=y, label=label), col="black")
plot = plot + geom_label(data=df_auc_label, aes(x=0.9, y=y, label=label, col=methode), size = 2.5,label.padding = unit(0.15, "lines"))
plot = plot + geom_label(data=df_auc_leg, aes(x=x, y=y, label=label), col="black", size = 2.5,label.padding = unit(0.15, "lines"))
}
plot = plot + geom_hline( aes(yintercept = 0.9), col="black" , size = 0.5, show.legend = NA,linetype="dashed")
plot = plot + facet_grid(. ~ couple )
......@@ -698,8 +709,8 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
save_plot(paste0(opt$out,suffix,".recall_precision_ok.pdf"),
plot_recall_precision_papier_ok,
ncol = 4,
nrow = 4,
ncol = 2,
nrow = 3,
base_aspect_ratio = 1,
limitsize = FALSE
)
......
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