add final sens spe plot

lib/pipeline.ml

@@ -265,7 +265,7 @@ let validation_main ~outdir ?(indir = "") ?(ns = 0) ?(np = 2) ?(mem = 2) ~previe
   let simu_dataset_l = derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns ~no_Ne ~no_HaPC in
   let post_analyses_simu = Post_analyses.post_analyses_simu_of_simu_dataset_l ~simu_dataset_l in
   let repo_of_post_analyses_simu = Post_analyses.repo_of_post_analyses_simu ~post_analyses_simu in
-  let repo_per_tree_simu = List.map trees ~f:(fun tree ->
+  let repo_and_post_analyses_per_tree_simu = List.map trees ~f:(fun tree -> (*to keep together all models per tree*)
       let trees = [tree] in
       let tree_prefix = Filename.chop_extension tree in
       let dataset_l =
@@ -283,9 +283,13 @@ let validation_main ~outdir ?(indir = "") ?(ns = 0) ?(np = 2) ?(mem = 2) ~previe
         Repo.shift tree_prefix (Post_analyses.repo_of_post_analyses_res ~prefix:tree_prefix ~post_analyses_res);
       ] |> List.concat
       in
-      repo_per_tree
-    ) |> List.concat
+      (repo_per_tree, post_analyses_res)
+    )
   in
+  let all_repo_per_tree_simu = List.map repo_and_post_analyses_per_tree_simu ~f:(fun (r,p) -> r) |> List.concat in
+  let all_post_analyses_per_tree = List.map repo_and_post_analyses_per_tree_simu ~f:(fun (r,p) -> p) in
+  let profile = Filename.chop_extension profile_fn in
+  let repo_post_analyses_all_trees = Post_analyses.repo_post_analyses_all_trees_of_all_post_analyses_per_tree ~all_post_analyses_per_tree ~profile in
   (* real trees *)
   let indir_dataset_l = if indir = "" then [] else parse_input_data indir in
   let dataset_l = indir_dataset_l in
@@ -300,7 +304,7 @@ let validation_main ~outdir ?(indir = "") ?(ns = 0) ?(np = 2) ?(mem = 2) ~previe
     repo_of_dataset_results_l ~dataset_results_l ;
   ] |> List.concat
   in
-  let repo = repo_of_post_analyses_simu @ repo_real_trees @ repo_per_tree_simu in
+  let repo = repo_of_post_analyses_simu @ repo_real_trees @ all_repo_per_tree_simu @repo_post_analyses_all_trees in
   Repo.build ~outdir ~np ~mem:(`GB mem) ~logger repo
 
 let simulation_command =

lib/post_analyses.ml

@@ -7,11 +7,13 @@ open File_formats
 open Convergence_detection
 
 type post_analyses_dir
+type sens_spe_t_choices_plot
 
 type t_choices = {
   t_choices_complete: text_file workflow ;
   t_choices_max: text_file workflow ;
   t_choices_plot: text_file workflow ;
+  tree_prefix: string;
 }
 
 type auto_t_plot = {
@@ -24,6 +26,7 @@ type auto_t_plot = {
 type post_analyses_res = {
   t_choices : t_choices option;
   auto_t_plot_l : auto_t_plot list option;
+  dataset_results_l : dataset_res list;
 }
 
 type simu_infos = {
@@ -106,7 +109,8 @@ let get_t_choices ~(dataset_results_l: dataset_res list) : t_choices option =
     let t_choices_max = t_choices_dir / selector ["out.max_per_meth.tsv"] in
     let t_choices_complete = t_choices_dir / selector ["out.complete.tsv"] in
     let t_choices_plot = t_choices_dir / selector ["out.pdf"] in
-    Some {t_choices_max; t_choices_complete ; t_choices_plot}
+    let tree_prefix = h0.tree_prefix in
+    Some {t_choices_max; t_choices_complete ; t_choices_plot; tree_prefix}
   | _ -> None
 
 
@@ -144,7 +148,7 @@ let get_simu_infos ~(dataset:Dataset.t) =
 let post_analyses_res_of_dataset_results_l ~dataset_results_l =
   let t_choices = get_t_choices ~dataset_results_l in
   let auto_t_plot_l = plot_det_meth_res_auto_t ~t_choices ~dataset_results_l in
-  {t_choices; auto_t_plot_l}
+  {t_choices; auto_t_plot_l;dataset_results_l}
 
 let post_analyses_simu_of_simu_dataset_l ~simu_dataset_l =
   let simu_infos_l = List.map simu_dataset_l ~f:(fun dataset ->
@@ -156,6 +160,60 @@ let post_analyses_simu_of_simu_dataset_l ~simu_dataset_l =
   let simu_infos_plot = group_simu_infos ~simu_infos_l / selector ["out.pdf"] in
   {simu_infos_l; simu_infos_plot}
 
+
+
+let plot_sens_spe_t_choices ~t_choices_l ~dataset_results_l ~profile : sens_spe_t_choices_plot directory workflow =
+  let env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07162018" () in
+  let t_choices_dir = tmp // "t_choices_dir" in
+  let merged_results_dir = tmp // "merged_results_dir" in
+  let out = dest // "out" in
+  let cmd_cp_t_choices_l = List.map t_choices_l ~f:(fun t_choices ->
+      cmd "cp" [dep t_choices.t_choices_max ; t_choices_dir // (t_choices.tree_prefix ^ ".tsv")]
+    )
+  in
+  let cmd_cp_merged_results_l = List.map dataset_results_l ~f:(fun dataset_results ->
+      cmd "cp" [dep dataset_results.merged_results ; merged_results_dir // (dataset_results.tree_prefix ^"@"^ dataset_results.model_prefix ^ ".tsv")]
+    )
+  in
+  workflow ~descr:"post_analyses.plot_sens_spe_all_trees" [
+    docker env (
+      and_list ([
+          [mkdir_p dest];
+          [mkdir_p t_choices_dir ];
+          [mkdir_p merged_results_dir ];
+          cmd_cp_t_choices_l;
+          cmd_cp_merged_results_l;
+          [cmd "Rscript" [
+              file_dump (string Scripts.plot_sens_spe_all_trees) ;
+              opt "--input_dir" ident t_choices_dir;
+              opt "--input_dir2" ident merged_results_dir;
+              opt "--profil" string profile;
+              opt "--out " ident out;
+            ];]
+        ]
+          |> List.concat)
+    )
+  ]
+
+let repo_post_analyses_all_trees_of_all_post_analyses_per_tree ~profile ~all_post_analyses_per_tree =
+  let t_choices_l = List.map all_post_analyses_per_tree ~f:(fun post_analyses_res ->
+      match post_analyses_res.t_choices with
+      | Some w -> [w]
+      | None -> []
+    ) |> List.concat
+  in
+  let dataset_results_l =  List.map all_post_analyses_per_tree ~f:(fun post_analyses_res ->
+      post_analyses_res.dataset_results_l) |> List.concat
+  in
+  let sens_spe_t_choices_plot = plot_sens_spe_t_choices  ~t_choices_l ~dataset_results_l ~profile in
+  Repo.[
+    item ["sens_spe.pdf"] (sens_spe_t_choices_plot / selector ["out.sens_spe_auto_t.pdf"]);
+    item ["all_t_choices.pdf"] (sens_spe_t_choices_plot / selector ["out.max_t_per_tree.pdf"]);
+    item ["sens_spe.tsv"] (sens_spe_t_choices_plot / selector ["out.sens_spe_auto_t.tsv"]);
+    item ["all_t_choices.tsv"] (sens_spe_t_choices_plot / selector ["out.max_t_per_tree.tsv"]);
+  ]
+
+
 let repo_of_post_analyses_simu ~post_analyses_simu =
   [
     Repo.[