Convergence_detection: introduced simpler utility to plot alignments

lib/convergence_detection.ml

@@ -147,3 +147,21 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
     ]
   in
   Workflow.select inner ["results.svg"]
+
+let plot_convergent_sites ?(plot_all_sites = true) ~alignment ~detection_results ~tree () =
+  Workflow.shell ~descr:"plot_convergent_sites.py" [
+    within_container Pcoc.img (
+      and_list [
+        mkdir_p dest ;
+        cmd "python" [
+          Utils.script_dump Scripts.[ diffsel_script_utils ; plot_data ; plot_convergent_sites ] ;
+          opt "-tsv" dep detection_results ;
+          opt "-msa" dep alignment ;
+          opt "-tree" dep tree ;
+          opt "-out" ident (dest // "plot.svg") ;
+          flag string "--all_sites" plot_all_sites ;
+        ]
+      ]
+    )
+  ]
+  |> Fn.flip Workflow.select ["plot.svg"]

lib/convergence_detection.mli

@@ -41,3 +41,11 @@ val plot_merge_results :
   tsv:text_file pworkflow ->
   unit ->
   svg pworkflow
+
+val plot_convergent_sites :
+  ?plot_all_sites:bool ->
+  alignment:aminoacid_fasta pworkflow ->
+  detection_results:text_file pworkflow ->
+  tree:nhx pworkflow ->
+  unit ->
+  svg pworkflow

lib/debug.ml

@@ -25,6 +25,10 @@ let less w =
   Sys.command (sprintf "less %s" (path w))
   |> ignore
 
+let firefox w =
+  Sys.command (sprintf "firefox %s" (path w))
+  |> ignore
+
 let workflow_of_template t =
   let open Bistro.Shell_dsl in
   Workflow.shell [

lib/pipeline2.ml

@@ -104,3 +104,10 @@ let diffseldsparse d =
     ~w_every:1
     ~n_cycles:50
     ()
+
+let alignment_plot d =
+  Convergence_detection.plot_convergent_sites
+    ~tree:(tree d)
+    ~alignment:(amino_acid_alignment d)
+    ~detection_results:(multinomial d)
+    ()