Skip to content

GitLab

Commit 6481fe5d authored by Carine Rey's avatar Carine Rey
Browse files

add NeG1_NeC_5 NeG5_NeC_1

parent 6145bbaf
Hide whitespace changes
Inline Side-by-side
Showing with 86 additions and 4 deletions
lib/convergence_hypothesis.ml
View file @ 6481fe5d
......@@ -18,7 +18,10 @@ type t =
| HaPCOC
| HaPC_NeG5_NeC_div2
| HaPC_NeG5_NeC_x2
| HaPC_NeG1_NeC_5
| HaPC_NeG5_NeC_1
| H0_NeG1_NeC_5
| H0_NeG5_NeC_1
let string_of_model m = match m with
| H0_NeG1 -> "H0_NeG1"
......@@ -36,6 +39,10 @@ let string_of_model m = match m with
| 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_NeG1_NeC_5"
| HaPC_NeG5_NeC_1 -> "HaPC_NeG5_NeC_1"
| H0_NeG1_NeC_5 -> "H0_NeG1_NeC_5"
| H0_NeG5_NeC_1 -> "H0_NeG5_NeC_1"
let assign k v =
seq ~sep:"=" [ string k ; v ]
......@@ -106,5 +113,9 @@ let bpp_config_F nodes hyp = [
| HaPC_NeG5_NeC_x2 -> bpp_config_HaPC_F_Ne
| H0_NeG5_NeC_div2 -> bpp_config_H0_F_Ne
| H0_NeG5_NeC_x2 -> bpp_config_H0_F_Ne
| HaPC_NeG1_NeC_5 -> bpp_config_HaPC_F_Ne
| HaPC_NeG5_NeC_1 -> bpp_config_HaPC_F_Ne
| H0_NeG1_NeC_5 -> bpp_config_H0_F_Ne
| H0_NeG5_NeC_1 -> bpp_config_H0_F_Ne
;
]
lib/pipeline.ml
View file @ 6481fe5d
......@@ -77,6 +77,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
| HaPC_NeG5_NeC_x2 -> 5.
| H0_NeG5_NeC_div2 -> 5.
| H0_NeG5_NeC_x2 -> 5.
| HaPC_NeG1_NeC_5 -> 1.
| HaPC_NeG5_NeC_1 -> 5.
| H0_NeG1_NeC_5 -> 1.
| H0_NeG5_NeC_1 -> 5.
| _ -> 1.
in
let ne_c = match model with
......@@ -94,6 +98,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
| HaPC_NeG5_NeC_x2 -> ne_g *. 2.
| H0_NeG5_NeC_div2 -> ne_g /. 2.
| H0_NeG5_NeC_x2 -> ne_g *. 2.
| HaPC_NeG1_NeC_5 -> 5.
| HaPC_NeG5_NeC_1 -> 1.
| H0_NeG1_NeC_5 -> 5.
| H0_NeG5_NeC_1 -> 1.
| _ -> ne_g
in
let ne_a = match model with
......@@ -111,6 +119,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
| HaPC_NeG5_NeC_x2 -> ne_g
| H0_NeG5_NeC_div2 -> ne_g
| H0_NeG5_NeC_x2 -> ne_g
| HaPC_NeG1_NeC_5 -> ne_g
| HaPC_NeG5_NeC_1 -> ne_g
| H0_NeG1_NeC_5 -> ne_g
| H0_NeG5_NeC_1 -> ne_g
| _ -> ne_g
in
let profile_f = profile.profile_f in
......@@ -160,6 +172,10 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
HaPC_NeG5_NeC_x2 ;
H0_NeG5_NeC_div2 ;
H0_NeG5_NeC_x2 ;
HaPC_NeG1_NeC_5 ;
HaPC_NeG5_NeC_1 ;
H0_NeG1_NeC_5 ;
H0_NeG5_NeC_1 ;
]
);
(if ne_test then
......
lib/post_analyses.ml
View file @ 6481fe5d
......@@ -70,6 +70,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~h0_NeG5_NeC_div2_mr
~h0_NeG5_NeC_x2_mr
~h0_NeG5_indel_mr
~haPC_NeG5_NeC_1_mr
~haPC_NeG1_NeC_5_mr
~h0_NeG1_NeC_5_mr
~h0_NeG5_NeC_1_mr
~haPC_NeG5_indel_mr () : post_analyses_dir directory workflow =
let env = Env.env_r in
......@@ -89,6 +93,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
("--HaPC_NeG5_NeC_x2_res" , haPC_NeG5_NeC_x2_mr );
("--H0_NeG5_NeC_div2_res" , h0_NeG5_NeC_div2_mr );
("--H0_NeG5_NeC_x2_res" , h0_NeG5_NeC_x2_mr );
("--HaPC_NeG5_NeC_1_res" , haPC_NeG5_NeC_1_mr );
("--H0_NeG5_NeC_1_res" , h0_NeG5_NeC_1_mr );
("--HaPC_NeG1_NeC_5_res" , haPC_NeG1_NeC_5_mr );
("--H0_NeG1_NeC_5_res" , h0_NeG1_NeC_5_mr );
("--H0_NeG5_indel_res" , h0_NeG5_indel_mr);
("--HaPC_NeG5_indel_res" , haPC_NeG5_indel_mr );
("--HaPCOC" , haPCOC_mr );
......@@ -193,6 +201,11 @@ type res_all_hyp = {
h0_NeG5_NeC_div2_res : dataset_res option ;
h0_NeG5_NeC_x2_res : dataset_res option ;
haPC_NeG5_NeC_1_res : dataset_res option ;
haPC_NeG1_NeC_5_res : dataset_res option ;
h0_NeG5_NeC_1_res : dataset_res option ;
h0_NeG1_NeC_5_res : dataset_res option ;
h0_NeG5_indel_res : dataset_res option ;
haPC_NeG5_indel_res : dataset_res option ;
}
......@@ -208,6 +221,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_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_NeG5_NeC_1_res ;
h0_NeG1_NeC_5_res ;
h0_NeG5_indel_res;
haPC_NeG5_indel_res;
} =
......@@ -230,6 +247,11 @@ 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_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_NeG1_NeC_5_mr = get_merged_results_opt haPC_NeG1_NeC_5_res in
let h0_NeG1_NeC_5_mr = get_merged_results_opt h0_NeG1_NeC_5_res in
let h0_NeG5_NeC_1_mr = get_merged_results_opt h0_NeG5_NeC_1_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
......@@ -250,6 +272,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
~h0_NeG5_NeC_x2_mr
~h0_NeG5_indel_mr
~haPC_NeG5_indel_mr
~haPC_NeG5_NeC_1_mr
~haPC_NeG1_NeC_5_mr
~h0_NeG1_NeC_5_mr
~h0_NeG5_NeC_1_mr
()
......@@ -272,6 +298,11 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let haPC_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_x2" ) 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 haPC_NeG5_NeC_1_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_1" ) in
let haPC_NeG1_NeC_5_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG1_NeC_5" ) in
let h0_NeG5_NeC_1_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_1" ) in
let h0_NeG1_NeC_5_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG1_NeC_5" ) 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
......@@ -283,6 +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;
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_1_res; haPC_NeG1_NeC_5_res; h0_NeG1_NeC_5_res; h0_NeG5_NeC_1_res;
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_recall09 = t_choices_dir / selector ["out.recall09_per_meth.tsv"] in
......
lib/scripts/calc_t_per_meth.R
View file @ 6481fe5d
......@@ -25,6 +25,11 @@ 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("--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("--HaPC_NeG5_NeC_1_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_NeC_1_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("--HaPC_NeG1_NeC_5_res" ) , type="character", default=NA, help="merged_results HaPC_NeG1_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_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"),
......@@ -85,6 +90,11 @@ 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_x2 = read_hyp(opt$H0_NeG5_NeC_x2 )
df_HaPC_NeG5_NeC_1 = read_hyp(opt$HaPC_NeG5_NeC_1)
df_H0_NeG5_NeC_1 = read_hyp(opt$H0_NeG5_NeC_1 )
df_HaPC_NeG1_NeC_5 = read_hyp(opt$HaPC_NeG1_NeC_5 )
df_H0_NeG1_NeC_5 = read_hyp(opt$H0_NeG1_NeC_5 )
df_HaPC_NeG5_indel = read_hyp(opt$HaPC_NeG5_indel_res )
df_H0_NeG5_indel = read_hyp(opt$H0_NeG5_indel_res )
......@@ -123,6 +133,9 @@ df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG
df_d_H0HaPC_NeG5_NeC_div2 = build_df_dist_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
df_d_H0HaPC_NeG5_NeC_x2 = build_df_dist_couple(df_H0_NeG5_NeC_x2, df_HaPC_NeG5_NeC_x2, "H0/HaPC NeG5_NeC_x2")
df_d_H0HaPC_NeG5_NeC_1 = build_df_dist_couple(df_H0_NeG5_NeC_1, df_HaPC_NeG5_NeC_1, "H0/HaPC NeG5_NeC_1")
df_d_H0HaPC_NeG1_NeC_5 = build_df_dist_couple(df_H0_NeG1_NeC_5, df_HaPC_NeG1_NeC_5, "H0/HaPC NeG5_NeC_5")
df_d_H0HaPC_NeG5_indel = build_df_dist_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel")
df_d = rbind.data.frame(
......@@ -134,6 +147,8 @@ df_d = rbind.data.frame(
df_d_H0HaPC_NeG5,
df_d_H0HaPC_NeG5_NeC_div2,
df_d_H0HaPC_NeG5_NeC_x2,
df_d_H0HaPC_NeG5_NeC_1,
df_d_H0HaPC_NeG1_NeC_5,
df_d_H0HaPC_NeG5_indel
)
......@@ -212,11 +227,15 @@ df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5")
df_H0HaPC_NeG5_NeC_div2 = build_df_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
df_H0HaPC_NeG5_NeC_x2 = build_df_couple(df_H0_NeG5_NeC_x2, df_HaPC_NeG5_NeC_x2, "H0/HaPC NeG5_NeC_x2")
df_H0HaPC_NeG5_NeC_1 = build_df_couple(df_H0_NeG5_NeC_1, df_HaPC_NeG5_NeC_1, "H0/HaPC NeG5_NeC_1")
df_H0HaPC_NeG1_NeC_5 = build_df_couple(df_H0_NeG1_NeC_5, df_HaPC_NeG1_NeC_5, "H0/HaPC NeG1_NeC_5")
df_H0HaPC_NeG5_indel = build_df_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel")
df_l = list(df_H0HaPCOC_NeG1, df_H0HaPC_NeG1, df_H0HaPC_NeG2, df_H0HaPC_NeG3,
df_H0HaPC_NeG4, df_H0HaPC_NeG5, df_H0HaPC_NeG5_NeC_div2,
df_H0HaPC_NeG5_NeC_1,df_H0HaPC_NeG1_NeC_5,
df_H0HaPC_NeG5_NeC_x2,df_H0HaPC_NeG5_indel)
df_l = df_l[-which(sapply(df_l, is.null))]
......@@ -302,8 +321,8 @@ print(df_recall_sup09_per_meth)
plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffix="") {
nb_c = length(unique(df_out$couple))
colors = c(c("#984EA3","#4AA947","#377EB8","#E41A1C","#F5BE5B","#90EE90","#8B6914","#BFBFBF")[1:nb_c], c("#7F7F7F","#ADD8E6"))
colors2 = c("#984EA3","#4AA947","#377EB8","#E41A1C","#F5BE5B","#90EE90","#8B6914","#7F7F7F","#ADD8E6")
colors = c(c("#984EA3","#4AA947","#377EB8","#E41A1C","#F5BE5B","#90EE90","#8B6914","#BFBFBF","#0000FF","#FFC0CB")[1:nb_c], c("#7F7F7F","#ADD8E6"))
colors2 = c("#984EA3","#4AA947","#377EB8","#E41A1C","#F5BE5B","#90EE90","#8B6914","#BFBFBF","#7F7F7F","#ADD8E6")
if (! is.null(meths)) {
df_out = df_out[df_out$methode %in%meths,]
......@@ -360,7 +379,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
)
print("plot recall_precision")
if (length(meths) <= 7) {
if (length(meths) <= 9) {
plot = ggplot(df_out, aes(x=sensitivity, y=precision98_02, col = methode))
plot = plot + theme_bw()
plot = plot + labs(x="Sensitivity (= Recall)", y="Precision (98/2)")
......
lib/tree_dataset.ml
View file @ 6481fe5d
......@@ -32,6 +32,10 @@ let nodes dataset (model : Convergence_hypothesis.t) =
|H0_NeG5_NeC_div2 -> [ "tree.H0_a.node_ids" ]
|H0_NeG5_NeC_x2 -> [ "tree.H0_a.node_ids" ]
|HaPCOC -> [ "tree.Ha.node_ids" ]
|HaPC_NeG1_NeC_5 -> [ "tree.Ha.node_ids" ]
|HaPC_NeG5_NeC_1 -> [ "tree.Ha.node_ids" ]
|H0_NeG1_NeC_5 -> [ "tree.H0_a.node_ids" ]
|H0_NeG5_NeC_1 -> [ "tree.H0_a.node_ids" ]
)
let tree dataset mode =
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment