Commit 97a4171c authored by Louis Duchemin's avatar Louis Duchemin
Browse files

Benchmark on Mutsel with CpG hypermutability

parent 19ffabff
......@@ -65,16 +65,16 @@ let hist_pval (convergence_table : cpt file) (pvalue_column:string): pdf file =
Bistro.Workflow.path_plugin ~descr:"Calibration.hist_pval" f
(* let quantiles_pval convergence_table pvalue_column =
let module R = Bistro_utils.R_script in
let f = fun%workflow dest ->
let module R = Bistro_utils.R_script in
let f = fun%workflow dest ->
let pvals = pvals_of_cpt [%path convergence_table] pvalue_column
|> Array.to_list in
[%script {|
library(tidyverse)
pvals = <<< R.(make [floats pvals]) >>>
|}] in
let script = Workflow.path_plugin ~descr:"calibration.quantiles_pval_script" f in
R.workflow ~descr:"calibration.quantiles_pval" f *)
let script = Workflow.path_plugin ~descr:"calibration.quantiles_pval_script" f in
R.workflow ~descr:"calibration.quantiles_pval" f *)
module Under_mutsel = struct
module Pipeline = Codepi.Simulation_pipeline.Mutsel
......@@ -89,7 +89,7 @@ module Under_mutsel = struct
{ f ; label ; requires_rooted_tree }
let methods = Pipeline.[
meth tdg09 "tdg09" ;
(* meth tdg09 "tdg09" ; *)
meth inhouse_tdg09 "inhouse_tdg09" ;
(* meth pcoc "pcoc" ; *)
(* meth pcoc_v2 ~col:3 "pcoc v2" ; *)
......@@ -130,8 +130,8 @@ module Under_mutsel = struct
~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
~n_h0:9000 ~n_ha:1000 ()
let benchmark dataset =
let q = query_benchmark dataset in
let benchmark dataset ?(query_builder = query_benchmark) () =
let q = query_builder dataset in
let methods = List.filter_map methods ~f:(fun m ->
if not m.requires_rooted_tree || dataset.rooted then
Some m.f else None
......@@ -231,8 +231,20 @@ let target () =
let multinomial_under_mutsel_besnard2009 = Under_mutsel.multinomial besnard2009 in
let _tdg09_under_mutsel_besnard2009 = Under_mutsel.tdg09 besnard2009 in
let inhouse_tdg09_under_mutsel_besnard2009 = Under_mutsel.inhouse_tdg09 besnard2009 in
print_endline "Benchmark besnard";
let benchmark_besnard = Under_mutsel.(benchmark besnard2009 |> plot_benchmark) in
let benchmark_besnard = Under_mutsel.(benchmark besnard2009 ()|> plot_benchmark) in
print_endline "Benchmark besnard with CpG";
let query_benchmark_CpG ?(seed = 42) { tree = t ; ne_s ; branch_scale ; _ } =
let module Pipeline = Codepi.Simulation_pipeline.Mutsel in
Pipeline.query ~seed ~tree:(NHX t) ~branch_scale ~ne_s
~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
~n_h0:9000 ~n_ha:1000 () in
let benchmark_besnard_CpG = Under_mutsel.(
benchmark besnard2009 ~query_builder:query_benchmark_CpG ()|> plot_benchmark
) in
print_endline "Benchmark rubisco";
let benchmark_echolocation = Under_mutsel.(benchmark rubisco |> plot_benchmark) in
let benchmark_echolocation = Under_mutsel.(benchmark rubisco () |> plot_benchmark) in
Report.pdflatex [%include_script "notes/calibration.tex"]
......@@ -44,14 +44,17 @@
\includegraphics[width=0.75\textwidth]{<<<Report.pdfdep benchmark_besnard>>>}
\end{frame}
\begin{frame}{Benchmark Echolocation under Mutsel}
\includegraphics[width=0.75\textwidth]{<<<Report.pdfdep benchmark_echolocation>>>}
\end{frame}
% \begin{frame}{Benchmark Echolocation under Mutsel}
% \includegraphics[width=0.75\textwidth]{<<<Report.pdfdep benchmark_echolocation>>>}
% \end{frame}
\subsection{Mutsel model with gBGC}
% for each topology
\subsection{Mutsel model with CpG hypermutability}
% for each topology
\begin{frame}{Benchmark Besnard2009 under Mutsel}
\includegraphics[width=0.75\textwidth]{<<<Report.pdfdep benchmark_besnard_CpG>>>}
\end{frame}
\end{document}
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