Commit ed2857b1 authored by Carine Rey's avatar Carine Rey
Browse files

try NeG5_NeC_2.5 et NeG2.5_NeC5

parent dae465e1
...@@ -18,10 +18,10 @@ type t = ...@@ -18,10 +18,10 @@ type t =
| HaPCOC | HaPCOC
| HaPC_NeG5_NeC_div2 | HaPC_NeG5_NeC_div2
| HaPC_NeG5_NeC_x2 | HaPC_NeG5_NeC_x2
| HaPC_NeG1_NeC_5 | HaPC_NeG2_NeC_5
| HaPC_NeG5_NeC_1 | HaPC_NeG5_NeC_2
| H0_NeG1_NeC_5 | H0_NeG2_NeC_5
| H0_NeG5_NeC_1 | H0_NeG5_NeC_2
let string_of_model m = match m with let string_of_model m = match m with
| H0_NeG1 -> "H0_NeG1" | H0_NeG1 -> "H0_NeG1"
...@@ -39,10 +39,10 @@ let string_of_model m = match m with ...@@ -39,10 +39,10 @@ let string_of_model m = match m with
| HaPC_NeG5_NeC_x2 -> "HaPC_NeG5_NeC_x2" | HaPC_NeG5_NeC_x2 -> "HaPC_NeG5_NeC_x2"
| H0_NeG5_NeC_div2 -> "H0_NeG5_NeC_div2" | H0_NeG5_NeC_div2 -> "H0_NeG5_NeC_div2"
| H0_NeG5_NeC_x2 -> "H0_NeG5_NeC_x2" | H0_NeG5_NeC_x2 -> "H0_NeG5_NeC_x2"
| HaPC_NeG1_NeC_5 -> "HaPC_NeG1_NeC_5" | HaPC_NeG2_NeC_5 -> "HaPC_NeG2_NeC_5"
| HaPC_NeG5_NeC_1 -> "HaPC_NeG5_NeC_1" | HaPC_NeG5_NeC_2 -> "HaPC_NeG5_NeC_2"
| H0_NeG1_NeC_5 -> "H0_NeG1_NeC_5" | H0_NeG2_NeC_5 -> "H0_NeG2_NeC_5"
| H0_NeG5_NeC_1 -> "H0_NeG5_NeC_1" | H0_NeG5_NeC_2 -> "H0_NeG5_NeC_2"
let assign k v = let assign k v =
seq ~sep:"=" [ string k ; v ] seq ~sep:"=" [ string k ; v ]
...@@ -113,9 +113,9 @@ let bpp_config_F nodes hyp = [ ...@@ -113,9 +113,9 @@ let bpp_config_F nodes hyp = [
| HaPC_NeG5_NeC_x2 -> bpp_config_HaPC_F_Ne | HaPC_NeG5_NeC_x2 -> bpp_config_HaPC_F_Ne
| H0_NeG5_NeC_div2 -> bpp_config_H0_F_Ne | H0_NeG5_NeC_div2 -> bpp_config_H0_F_Ne
| H0_NeG5_NeC_x2 -> bpp_config_H0_F_Ne | H0_NeG5_NeC_x2 -> bpp_config_H0_F_Ne
| HaPC_NeG1_NeC_5 -> bpp_config_HaPC_F_Ne | HaPC_NeG2_NeC_5 -> bpp_config_HaPC_F_Ne
| HaPC_NeG5_NeC_1 -> bpp_config_HaPC_F_Ne | HaPC_NeG5_NeC_2 -> bpp_config_HaPC_F_Ne
| H0_NeG1_NeC_5 -> bpp_config_H0_F_Ne | H0_NeG2_NeC_5 -> bpp_config_H0_F_Ne
| H0_NeG5_NeC_1 -> bpp_config_H0_F_Ne | H0_NeG5_NeC_2 -> bpp_config_H0_F_Ne
; ;
] ]
...@@ -77,10 +77,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr ...@@ -77,10 +77,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
| HaPC_NeG5_NeC_x2 -> 5. | HaPC_NeG5_NeC_x2 -> 5.
| H0_NeG5_NeC_div2 -> 5. | H0_NeG5_NeC_div2 -> 5.
| H0_NeG5_NeC_x2 -> 5. | H0_NeG5_NeC_x2 -> 5.
| HaPC_NeG1_NeC_5 -> 1. | HaPC_NeG2_NeC_5 -> 2.5
| HaPC_NeG5_NeC_1 -> 5. | HaPC_NeG5_NeC_2 -> 5.
| H0_NeG1_NeC_5 -> 1. | H0_NeG2_NeC_5 -> 2.5
| H0_NeG5_NeC_1 -> 5. | H0_NeG5_NeC_2 -> 5.
| _ -> 1. | _ -> 1.
in in
let ne_c = match model with let ne_c = match model with
...@@ -98,10 +98,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr ...@@ -98,10 +98,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
| HaPC_NeG5_NeC_x2 -> ne_g *. 2. | HaPC_NeG5_NeC_x2 -> ne_g *. 2.
| H0_NeG5_NeC_div2 -> ne_g /. 2. | H0_NeG5_NeC_div2 -> ne_g /. 2.
| H0_NeG5_NeC_x2 -> ne_g *. 2. | H0_NeG5_NeC_x2 -> ne_g *. 2.
| HaPC_NeG1_NeC_5 -> 5. | HaPC_NeG2_NeC_5 -> 5.
| HaPC_NeG5_NeC_1 -> 1. | HaPC_NeG5_NeC_2 -> 2.5
| H0_NeG1_NeC_5 -> 5. | H0_NeG2_NeC_5 -> 5.
| H0_NeG5_NeC_1 -> 1. | H0_NeG5_NeC_2 -> 2.5
| _ -> ne_g | _ -> ne_g
in in
let ne_a = match model with let ne_a = match model with
...@@ -119,10 +119,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr ...@@ -119,10 +119,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
| HaPC_NeG5_NeC_x2 -> ne_g | HaPC_NeG5_NeC_x2 -> ne_g
| H0_NeG5_NeC_div2 -> ne_g | H0_NeG5_NeC_div2 -> ne_g
| H0_NeG5_NeC_x2 -> ne_g | H0_NeG5_NeC_x2 -> ne_g
| HaPC_NeG1_NeC_5 -> ne_g | HaPC_NeG2_NeC_5 -> ne_g
| HaPC_NeG5_NeC_1 -> ne_g | HaPC_NeG5_NeC_2 -> ne_g
| H0_NeG1_NeC_5 -> ne_g | H0_NeG2_NeC_5 -> ne_g
| H0_NeG5_NeC_1 -> ne_g | H0_NeG5_NeC_2 -> ne_g
| _ -> ne_g | _ -> ne_g
in in
let profile_f = profile.profile_f in let profile_f = profile.profile_f in
...@@ -172,10 +172,10 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n ...@@ -172,10 +172,10 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
HaPC_NeG5_NeC_x2 ; HaPC_NeG5_NeC_x2 ;
H0_NeG5_NeC_div2 ; H0_NeG5_NeC_div2 ;
H0_NeG5_NeC_x2 ; H0_NeG5_NeC_x2 ;
HaPC_NeG1_NeC_5 ; HaPC_NeG2_NeC_5 ;
HaPC_NeG5_NeC_1 ; HaPC_NeG5_NeC_2 ;
H0_NeG1_NeC_5 ; H0_NeG2_NeC_5 ;
H0_NeG5_NeC_1 ; H0_NeG5_NeC_2 ;
] ]
); );
(if ne_test then (if ne_test then
......
...@@ -70,10 +70,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr ...@@ -70,10 +70,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~h0_NeG5_NeC_div2_mr ~h0_NeG5_NeC_div2_mr
~h0_NeG5_NeC_x2_mr ~h0_NeG5_NeC_x2_mr
~h0_NeG5_indel_mr ~h0_NeG5_indel_mr
~haPC_NeG5_NeC_1_mr ~haPC_NeG5_NeC_2_mr
~haPC_NeG1_NeC_5_mr ~haPC_NeG2_NeC_5_mr
~h0_NeG1_NeC_5_mr ~h0_NeG2_NeC_5_mr
~h0_NeG5_NeC_1_mr ~h0_NeG5_NeC_2_mr
~haPC_NeG5_indel_mr () : post_analyses_dir directory workflow = ~haPC_NeG5_indel_mr () : post_analyses_dir directory workflow =
let env = Env.env_r in let env = Env.env_r in
...@@ -93,10 +93,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr ...@@ -93,10 +93,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
("--HaPC_NeG5_NeC_x2_res" , haPC_NeG5_NeC_x2_mr ); ("--HaPC_NeG5_NeC_x2_res" , haPC_NeG5_NeC_x2_mr );
("--H0_NeG5_NeC_div2_res" , h0_NeG5_NeC_div2_mr ); ("--H0_NeG5_NeC_div2_res" , h0_NeG5_NeC_div2_mr );
("--H0_NeG5_NeC_x2_res" , h0_NeG5_NeC_x2_mr ); ("--H0_NeG5_NeC_x2_res" , h0_NeG5_NeC_x2_mr );
("--HaPC_NeG5_NeC_1_res" , haPC_NeG5_NeC_1_mr ); ("--HaPC_NeG5_NeC_2_res" , haPC_NeG5_NeC_2_mr );
("--H0_NeG5_NeC_1_res" , h0_NeG5_NeC_1_mr ); ("--H0_NeG5_NeC_2_res" , h0_NeG5_NeC_2_mr );
("--HaPC_NeG1_NeC_5_res" , haPC_NeG1_NeC_5_mr ); ("--HaPC_NeG2_NeC_5_res" , haPC_NeG2_NeC_5_mr );
("--H0_NeG1_NeC_5_res" , h0_NeG1_NeC_5_mr ); ("--H0_NeG2_NeC_5_res" , h0_NeG2_NeC_5_mr );
("--H0_NeG5_indel_res" , h0_NeG5_indel_mr); ("--H0_NeG5_indel_res" , h0_NeG5_indel_mr);
("--HaPC_NeG5_indel_res" , haPC_NeG5_indel_mr ); ("--HaPC_NeG5_indel_res" , haPC_NeG5_indel_mr );
("--HaPCOC" , haPCOC_mr ); ("--HaPCOC" , haPCOC_mr );
...@@ -201,10 +201,10 @@ type res_all_hyp = { ...@@ -201,10 +201,10 @@ type res_all_hyp = {
h0_NeG5_NeC_div2_res : dataset_res option ; h0_NeG5_NeC_div2_res : dataset_res option ;
h0_NeG5_NeC_x2_res : dataset_res option ; h0_NeG5_NeC_x2_res : dataset_res option ;
haPC_NeG5_NeC_1_res : dataset_res option ; haPC_NeG5_NeC_2_res : dataset_res option ;
haPC_NeG1_NeC_5_res : dataset_res option ; haPC_NeG2_NeC_5_res : dataset_res option ;
h0_NeG5_NeC_1_res : dataset_res option ; h0_NeG5_NeC_2_res : dataset_res option ;
h0_NeG1_NeC_5_res : dataset_res option ; h0_NeG2_NeC_5_res : dataset_res option ;
h0_NeG5_indel_res : dataset_res option ; h0_NeG5_indel_res : dataset_res option ;
haPC_NeG5_indel_res : dataset_res option ; haPC_NeG5_indel_res : dataset_res option ;
...@@ -221,10 +221,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res; ...@@ -221,10 +221,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
haPC_NeG5_NeC_x2_res ; haPC_NeG5_NeC_x2_res ;
h0_NeG5_NeC_div2_res ; h0_NeG5_NeC_div2_res ;
h0_NeG5_NeC_x2_res ; h0_NeG5_NeC_x2_res ;
haPC_NeG5_NeC_1_res; haPC_NeG5_NeC_2_res;
haPC_NeG1_NeC_5_res ; haPC_NeG2_NeC_5_res ;
h0_NeG5_NeC_1_res ; h0_NeG5_NeC_2_res ;
h0_NeG1_NeC_5_res ; h0_NeG2_NeC_5_res ;
h0_NeG5_indel_res; h0_NeG5_indel_res;
haPC_NeG5_indel_res; haPC_NeG5_indel_res;
} = } =
...@@ -247,10 +247,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res; ...@@ -247,10 +247,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
let h0_NeG5_NeC_div2_mr = get_merged_results_opt h0_NeG5_NeC_div2_res in let h0_NeG5_NeC_div2_mr = get_merged_results_opt h0_NeG5_NeC_div2_res in
let h0_NeG5_NeC_x2_mr = get_merged_results_opt h0_NeG5_NeC_x2_res in let h0_NeG5_NeC_x2_mr = get_merged_results_opt h0_NeG5_NeC_x2_res in
let haPC_NeG5_NeC_1_mr = get_merged_results_opt haPC_NeG5_NeC_1_res in let haPC_NeG5_NeC_2_mr = get_merged_results_opt haPC_NeG5_NeC_2_res in
let haPC_NeG1_NeC_5_mr = get_merged_results_opt haPC_NeG1_NeC_5_res in let haPC_NeG2_NeC_5_mr = get_merged_results_opt haPC_NeG2_NeC_5_res in
let h0_NeG1_NeC_5_mr = get_merged_results_opt h0_NeG1_NeC_5_res in let h0_NeG2_NeC_5_mr = get_merged_results_opt h0_NeG2_NeC_5_res in
let h0_NeG5_NeC_1_mr = get_merged_results_opt h0_NeG5_NeC_1_res in let h0_NeG5_NeC_2_mr = get_merged_results_opt h0_NeG5_NeC_2_res in
let h0_NeG5_indel_mr = get_merged_results_opt h0_NeG5_indel_res in let h0_NeG5_indel_mr = get_merged_results_opt h0_NeG5_indel_res in
let haPC_NeG5_indel_mr = get_merged_results_opt haPC_NeG5_indel_res in let haPC_NeG5_indel_mr = get_merged_results_opt haPC_NeG5_indel_res in
...@@ -272,10 +272,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res; ...@@ -272,10 +272,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
~h0_NeG5_NeC_x2_mr ~h0_NeG5_NeC_x2_mr
~h0_NeG5_indel_mr ~h0_NeG5_indel_mr
~haPC_NeG5_indel_mr ~haPC_NeG5_indel_mr
~haPC_NeG5_NeC_1_mr ~haPC_NeG5_NeC_2_mr
~haPC_NeG1_NeC_5_mr ~haPC_NeG2_NeC_5_mr
~h0_NeG1_NeC_5_mr ~h0_NeG2_NeC_5_mr
~h0_NeG5_NeC_1_mr ~h0_NeG5_NeC_2_mr
() ()
...@@ -299,10 +299,10 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice ...@@ -299,10 +299,10 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let h0_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_div2" ) in let h0_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_div2" ) in
let h0_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_x2" ) in let h0_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_x2" ) in
let haPC_NeG5_NeC_1_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_1" ) in let haPC_NeG5_NeC_2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_2" ) in
let haPC_NeG1_NeC_5_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG1_NeC_5" ) in let haPC_NeG2_NeC_5_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG2_NeC_5" ) in
let h0_NeG5_NeC_1_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_1" ) in let h0_NeG5_NeC_2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_2" ) in
let h0_NeG1_NeC_5_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG1_NeC_5" ) in let h0_NeG2_NeC_5_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG2_NeC_5" ) in
let h0_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_0.33_i" ) in let h0_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_0.33_i" ) in
let haPC_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_0.33_i" ) in let haPC_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_0.33_i" ) in
...@@ -314,7 +314,7 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice ...@@ -314,7 +314,7 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res; h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res;
haPC_NeG1_res; haPC_NeG2_res;haPC_NeG3_res; haPC_NeG4_res; haPC_NeG5_res; haPC_NeG1_res; haPC_NeG2_res;haPC_NeG3_res; haPC_NeG4_res; haPC_NeG5_res;
haPC_NeG5_NeC_div2_res; haPC_NeG5_NeC_x2_res; h0_NeG5_NeC_div2_res; h0_NeG5_NeC_x2_res; haPC_NeG5_NeC_div2_res; haPC_NeG5_NeC_x2_res; h0_NeG5_NeC_div2_res; h0_NeG5_NeC_x2_res;
haPC_NeG5_NeC_1_res; haPC_NeG1_NeC_5_res; h0_NeG1_NeC_5_res; h0_NeG5_NeC_1_res; haPC_NeG5_NeC_2_res; haPC_NeG2_NeC_5_res; h0_NeG2_NeC_5_res; h0_NeG5_NeC_2_res;
h0_NeG5_indel_res;haPC_NeG5_indel_res} in h0_NeG5_indel_res;haPC_NeG5_indel_res} in
let t_choices_max = t_choices_dir / selector ["out.max_MCC_per_meth.tsv"] in let t_choices_max = t_choices_dir / selector ["out.max_MCC_per_meth.tsv"] in
let t_choices_recall09 = t_choices_dir / selector ["out.recall09_per_meth.tsv"] in let t_choices_recall09 = t_choices_dir / selector ["out.recall09_per_meth.tsv"] in
......
...@@ -25,10 +25,10 @@ option_list = list( ...@@ -25,10 +25,10 @@ option_list = list(
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("--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"), make_option(c("--H0_NeG5_NeC_div2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_div2_res" , metavar="character"),
make_option(c("--H0_NeG5_NeC_x2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_x2_res" , metavar="character"), make_option(c("--H0_NeG5_NeC_x2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_x2_res" , metavar="character"),
make_option(c("--HaPC_NeG5_NeC_1_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_NeC_1_res" , metavar="character"), make_option(c("--HaPC_NeG5_NeC_2_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_NeC_2_res" , metavar="character"),
make_option(c("--H0_NeG5_NeC_1_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_1_res" , metavar="character"), make_option(c("--H0_NeG5_NeC_2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_2_res" , metavar="character"),
make_option(c("--HaPC_NeG1_NeC_5_res" ) , type="character", default=NA, help="merged_results HaPC_NeG1_NeC_5_res" , metavar="character"), make_option(c("--HaPC_NeG2_NeC_5_res" ) , type="character", default=NA, help="merged_results HaPC_NeG2_NeC_5_res" , metavar="character"),
make_option(c("--H0_NeG1_NeC_5_res" ) , type="character", default=NA, help="merged_results H0_NeG1_NeC_5_res" , metavar="character"), make_option(c("--H0_NeG2_NeC_5_res" ) , type="character", default=NA, help="merged_results H0_NeG2_NeC_5_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("--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("--HaPC_NeG5_indel_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_indel_res" , metavar="character"),
...@@ -90,10 +90,10 @@ df_HaPC_NeG5_NeC_x2 = read_hyp(opt$HaPC_NeG5_NeC_x2 ) ...@@ -90,10 +90,10 @@ df_HaPC_NeG5_NeC_x2 = read_hyp(opt$HaPC_NeG5_NeC_x2 )
df_H0_NeG5_NeC_div2 = read_hyp(opt$H0_NeG5_NeC_div2 ) df_H0_NeG5_NeC_div2 = read_hyp(opt$H0_NeG5_NeC_div2 )
df_H0_NeG5_NeC_x2 = read_hyp(opt$H0_NeG5_NeC_x2 ) df_H0_NeG5_NeC_x2 = read_hyp(opt$H0_NeG5_NeC_x2 )
df_HaPC_NeG5_NeC_1 = read_hyp(opt$HaPC_NeG5_NeC_1) df_HaPC_NeG5_NeC_2 = read_hyp(opt$HaPC_NeG5_NeC_2)
df_H0_NeG5_NeC_1 = read_hyp(opt$H0_NeG5_NeC_1 ) df_H0_NeG5_NeC_2 = read_hyp(opt$H0_NeG5_NeC_2 )
df_HaPC_NeG1_NeC_5 = read_hyp(opt$HaPC_NeG1_NeC_5 ) df_HaPC_NeG2_NeC_5 = read_hyp(opt$HaPC_NeG2_NeC_5 )
df_H0_NeG1_NeC_5 = read_hyp(opt$H0_NeG1_NeC_5 ) df_H0_NeG2_NeC_5 = read_hyp(opt$H0_NeG2_NeC_5 )
df_HaPC_NeG5_indel = read_hyp(opt$HaPC_NeG5_indel_res ) df_HaPC_NeG5_indel = read_hyp(opt$HaPC_NeG5_indel_res )
df_H0_NeG5_indel = read_hyp(opt$H0_NeG5_indel_res ) df_H0_NeG5_indel = read_hyp(opt$H0_NeG5_indel_res )
...@@ -113,6 +113,7 @@ build_df_dist_couple = function (df_h0,df_ha,name) { ...@@ -113,6 +113,7 @@ build_df_dist_couple = function (df_h0,df_ha,name) {
id_vars = if ("P_JSD" %in% colnames(df_h0)) {c("Sites","P_JSD","P_ED", "C1", "C2", "entropy_C1","entropy_C2")} else {c("Sites")} id_vars = if ("P_JSD" %in% colnames(df_h0)) {c("Sites","P_JSD","P_ED", "C1", "C2", "entropy_C1","entropy_C2")} else {c("Sites")}
df_h0 = melt(df_h0, id.vars = id_vars, variable.name = "methode") df_h0 = melt(df_h0, id.vars = id_vars, variable.name = "methode")
df_ha = melt(df_ha, id.vars = id_vars, variable.name = "methode") df_ha = melt(df_ha, id.vars = id_vars, variable.name = "methode")
print(name)
print(head(df_h0)) print(head(df_h0))
df = merge(df_h0, df_ha, by = c(id_vars, "methode"), suffix = c("_H0","_Ha")) df = merge(df_h0, df_ha, by = c(id_vars, "methode"), suffix = c("_H0","_Ha"))
df_melt = melt(df, id.vars = c(id_vars, "methode"), variable.name = "val_H0Ha") df_melt = melt(df, id.vars = c(id_vars, "methode"), variable.name = "val_H0Ha")
...@@ -133,8 +134,8 @@ df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG ...@@ -133,8 +134,8 @@ df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG
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_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") 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")
df_d_H0HaPC_NeG5_NeC_1 = build_df_dist_couple(df_H0_NeG5_NeC_1, df_HaPC_NeG5_NeC_1, "H0/HaPC NeG5_NeC_1") df_d_H0HaPC_NeG5_NeC_2 = build_df_dist_couple(df_H0_NeG5_NeC_2, df_HaPC_NeG5_NeC_2, "H0/HaPC NeG5_NeC_2")
df_d_H0HaPC_NeG1_NeC_5 = build_df_dist_couple(df_H0_NeG1_NeC_5, df_HaPC_NeG1_NeC_5, "H0/HaPC NeG1_NeC_5") df_d_H0HaPC_NeG2_NeC_5 = build_df_dist_couple(df_H0_NeG2_NeC_5, df_HaPC_NeG2_NeC_5, "H0/HaPC NeG2_NeC_5")
df_d_H0HaPC_NeG5_indel = build_df_dist_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel") df_d_H0HaPC_NeG5_indel = build_df_dist_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel")
...@@ -147,8 +148,8 @@ df_d = rbind.data.frame( ...@@ -147,8 +148,8 @@ df_d = rbind.data.frame(
df_d_H0HaPC_NeG5, df_d_H0HaPC_NeG5,
df_d_H0HaPC_NeG5_NeC_div2, df_d_H0HaPC_NeG5_NeC_div2,
df_d_H0HaPC_NeG5_NeC_x2, df_d_H0HaPC_NeG5_NeC_x2,
df_d_H0HaPC_NeG5_NeC_1, df_d_H0HaPC_NeG5_NeC_2,
df_d_H0HaPC_NeG1_NeC_5, df_d_H0HaPC_NeG2_NeC_5,
df_d_H0HaPC_NeG5_indel df_d_H0HaPC_NeG5_indel
) )
...@@ -227,15 +228,15 @@ df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5") ...@@ -227,15 +228,15 @@ df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5")
df_H0HaPC_NeG5_NeC_div2 = build_df_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2") df_H0HaPC_NeG5_NeC_div2 = build_df_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
df_H0HaPC_NeG5_NeC_x2 = build_df_couple(df_H0_NeG5_NeC_x2, df_HaPC_NeG5_NeC_x2, "H0/HaPC NeG5_NeC_x2") df_H0HaPC_NeG5_NeC_x2 = build_df_couple(df_H0_NeG5_NeC_x2, df_HaPC_NeG5_NeC_x2, "H0/HaPC NeG5_NeC_x2")
df_H0HaPC_NeG5_NeC_1 = build_df_couple(df_H0_NeG5_NeC_1, df_HaPC_NeG5_NeC_1, "H0/HaPC NeG5_NeC_1") df_H0HaPC_NeG5_NeC_2 = build_df_couple(df_H0_NeG5_NeC_2, df_HaPC_NeG5_NeC_2, "H0/HaPC NeG5_NeC_2")
df_H0HaPC_NeG1_NeC_5 = build_df_couple(df_H0_NeG1_NeC_5, df_HaPC_NeG1_NeC_5, "H0/HaPC NeG1_NeC_5") df_H0HaPC_NeG2_NeC_5 = build_df_couple(df_H0_NeG2_NeC_5, df_HaPC_NeG2_NeC_5, "H0/HaPC NeG2_NeC_5")
df_H0HaPC_NeG5_indel = build_df_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel") 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_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_NeG5_NeC_div2,
df_H0HaPC_NeG5_NeC_1,df_H0HaPC_NeG1_NeC_5, df_H0HaPC_NeG5_NeC_2,df_H0HaPC_NeG2_NeC_5,
df_H0HaPC_NeG5_NeC_x2,df_H0HaPC_NeG5_indel) df_H0HaPC_NeG5_NeC_x2,df_H0HaPC_NeG5_indel)
df_l = df_l[-which(sapply(df_l, is.null))] df_l = df_l[-which(sapply(df_l, is.null))]
...@@ -500,7 +501,6 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi ...@@ -500,7 +501,6 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
print(head(df_out_melt2)) print(head(df_out_melt2))
df_out_melt2_dcast = dcast(df_out_melt2, methode + threshold ~ couple, value.var="FPR" ) df_out_melt2_dcast = dcast(df_out_melt2, methode + threshold ~ couple, value.var="FPR" )
print(head(df_out_melt2_dcast)) print(head(df_out_melt2_dcast))
print(df_out_melt2_dcast)
# complete values for not existing threshold between couple # complete values for not existing threshold between couple
...@@ -532,13 +532,10 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi ...@@ -532,13 +532,10 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
df_out_melt2_dcast$H0NeG5 = complete_value(df_out_melt2_dcast, "H0NeG5") df_out_melt2_dcast$H0NeG5 = complete_value(df_out_melt2_dcast, "H0NeG5")
df_out_melt2_dcast$H0NeG5_NeC_x2 = complete_value(df_out_melt2_dcast, "H0NeG5_NeC_x2") df_out_melt2_dcast$H0NeG5_NeC_x2 = complete_value(df_out_melt2_dcast, "H0NeG5_NeC_x2")
df_out_melt2_dcast$H0NeG5_NeC_div2 = complete_value(df_out_melt2_dcast, "H0NeG5_NeC_div2") df_out_melt2_dcast$H0NeG5_NeC_div2 = complete_value(df_out_melt2_dcast, "H0NeG5_NeC_div2")
print(df_out_melt2_dcast)
df_out_melt2_dcast$d_H0NeG5_NeC_x2_H0NeG5 = df_out_melt2_dcast$H0NeG5_NeC_x2 - df_out_melt2_dcast$H0NeG5 df_out_melt2_dcast$d_H0NeG5_NeC_x2_H0NeG5 = df_out_melt2_dcast$H0NeG5_NeC_x2 - df_out_melt2_dcast$H0NeG5
df_out_melt2_dcast$d_H0NeG5_NeC_div2_H0NeG5 = df_out_melt2_dcast$H0NeG5_NeC_div2 - df_out_melt2_dcast$H0NeG5 df_out_melt2_dcast$d_H0NeG5_NeC_div2_H0NeG5 = df_out_melt2_dcast$H0NeG5_NeC_div2 - df_out_melt2_dcast$H0NeG5
print(df_out_melt2_dcast)
df_out_melt2_dcast_melt = melt(df_out_melt2_dcast[,c("methode", "threshold","d_H0NeG5_NeC_x2_H0NeG5","d_H0NeG5_NeC_div2_H0NeG5")], id.vars= c("methode", "threshold")) df_out_melt2_dcast_melt = melt(df_out_melt2_dcast[,c("methode", "threshold","d_H0NeG5_NeC_x2_H0NeG5","d_H0NeG5_NeC_div2_H0NeG5")], id.vars= c("methode", "threshold"))
print(head(df_out_melt2_dcast_melt)) print(head(df_out_melt2_dcast_melt))
...@@ -607,13 +604,13 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi ...@@ -607,13 +604,13 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
) )
plot_value_JSD = NULL plot_value_JSD = NULL
if ( all( c("P_JSD","P_ED", "C1", "C2", "entropy_C1","entropy_C2") %in% colnames(df_d))){ if ( all( c("P_JSD","P_ED", "C1", "C2", "entropy_C1","entropy_C2") %in% colnames(df_d)) & (length(meths) <= 9) ){
print("plot value/distance") print("plot value/distance")
plot = ggplot(df_d, aes(y=P_JSD, x=value, shape = val_H0Ha, col = val_H0Ha)) plot = ggplot(subset(df_d, val_H0Ha == "value_Ha"), aes(y=P_JSD, x=value, shape = val_H0Ha, col = val_H0Ha))
plot = plot + theme_bw() plot = plot + theme_bw()
plot = plot + theme(legend.position="top") plot = plot + theme(legend.position="top")
plot = plot + labs(y="P JSD", x="Value") plot = plot + labs(y="P JSD", x="Value")
...@@ -627,7 +624,11 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi ...@@ -627,7 +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 + theme(axis.text.x = element_text(angle = 45, hjust = 1))
plot_value_JSD = plot plot_value_JSD = plot
plot = ggplot(df_d, aes(y=P_ED, x=value, shape = val_H0Ha, col = val_H0Ha))
print(head(df_d))
print(table(df_d$val_H0Ha,df_d$methode,df_d$couple))
plot = ggplot(subset(df_d, val_H0Ha == "value_Ha"), aes(y=P_ED, x=value, shape = val_H0Ha, col = val_H0Ha))
plot = plot + theme_bw() plot = plot + theme_bw()
plot = plot + theme(legend.position="top") plot = plot + theme(legend.position="top")
plot = plot + labs(y="P ED", x="Value") plot = plot + labs(y="P ED", x="Value")
......
...@@ -32,10 +32,10 @@ let nodes dataset (model : Convergence_hypothesis.t) = ...@@ -32,10 +32,10 @@ let nodes dataset (model : Convergence_hypothesis.t) =
|H0_NeG5_NeC_div2 -> [ "tree.H0_a.node_ids" ] |H0_NeG5_NeC_div2 -> [ "tree.H0_a.node_ids" ]
|H0_NeG5_NeC_x2 -> [ "tree.H0_a.node_ids" ] |H0_NeG5_NeC_x2 -> [ "tree.H0_a.node_ids" ]
|HaPCOC -> [ "tree.Ha.node_ids" ] |HaPCOC -> [ "tree.Ha.node_ids" ]
|HaPC_NeG1_NeC_5 -> [ "tree.Ha.node_ids" ] |HaPC_NeG2_NeC_5 -> [ "tree.Ha.node_ids" ]
|HaPC_NeG5_NeC_1 -> [ "tree.Ha.node_ids" ] |HaPC_NeG5_NeC_2 -> [ "tree.Ha.node_ids" ]
|H0_NeG1_NeC_5 -> [ "tree.H0_a.node_ids" ] |H0_NeG2_NeC_5 -> [ "tree.H0_a.node_ids" ]
|H0_NeG5_NeC_1 -> [ "tree.H0_a.node_ids" ] |H0_NeG5_NeC_2 -> [ "tree.H0_a.node_ids" ]
) )
let tree dataset mode = let tree dataset mode =
......
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