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Commit 9f1d5072 authored by Carine Rey's avatar Carine Rey
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clean_up hyp + news hyp NeC_div/x2 (continuation)

parent fde6c8ec
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Showing with 63 additions and 97 deletions
lib/post_analyses.ml
View file @ 9f1d5072
......@@ -63,10 +63,13 @@ let build_cmd_t_choices (opt_name : string) mr_option =
| Some x -> [opt opt_name dep x]
| None -> []
let make_t_choices ~h0_mr ~h0_NeBig_mr ~h0_NeSmall_mr ~haPCOC_mr ~haPC_mr ~haPC_NeBig_mr ~haPC_NeSmall_mr ~h0_NeBigInSmall_mr
~h0_NeSmallInBig_mr ~haPC_NeBigInSmall_mr ~haPC_NeSmallInBig_mr
let make_t_choices ~haPCOC_mr
~h0_NeG1_mr ~h0_NeG2_mr ~h0_NeG3_mr ~h0_NeG4_mr ~h0_NeG5_mr
~haPC_NeG1_mr ~haPC_NeG2_mr ~haPC_NeG3_mr ~haPC_NeG4_mr ~haPC_NeG5_mr () : post_analyses_dir directory workflow =
~haPC_NeG1_mr ~haPC_NeG2_mr ~haPC_NeG3_mr ~haPC_NeG4_mr ~haPC_NeG5_mr
~haPC_NeG5_NeC_div2_mr
~haPC_NeG5_NeC_x2_mr
~h0_NeG5_NeC_div2_mr
~h0_NeG5_NeC_x2_mr () : post_analyses_dir directory workflow =
let env = r_env in
let out = dest // "out" in
......@@ -81,17 +84,11 @@ let make_t_choices ~h0_mr ~h0_NeBig_mr ~h0_NeSmall_mr ~haPCOC_mr ~haPC_mr ~haPC_
("--HaPC_NeG3" , haPC_NeG3_mr );
("--HaPC_NeG4" , haPC_NeG4_mr );
("--HaPC_NeG5" , haPC_NeG5_mr );
("--H0" , h0_mr );
("--H0NeBig" , h0_NeBig_mr );
("--H0NeSmall" , h0_NeSmall_mr );
("--H0NeBigInSmall" , h0_NeBigInSmall_mr );
("--H0NeSmallInBig" , h0_NeSmallInBig_mr );
("--HaPC_NeG5_NeC_div2_res" , haPC_NeG5_NeC_div2_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 );
("--HaPCOC" , haPCOC_mr );
("--HaPC" , haPC_mr );
("--HaPCNeBig" , haPC_NeBig_mr );
("--HaPCNeSmall" , haPC_NeSmall_mr);
("--HaPCNeBigInSmall" , haPC_NeBigInSmall_mr );
("--HaPCNeSmallInBig" , haPC_NeSmallInBig_mr);
] ~f:(fun (opt_name, mr_option) -> build_cmd_t_choices opt_name mr_option)
|> List.concat in
workflow ~descr:"post_analyses.t_choices" [
......@@ -176,17 +173,7 @@ let get_merged_results_opt hx = match hx with
| None -> None
type res_all_hyp = {
h0_res : dataset_res option ;
h0_NeBig_res : dataset_res option ;
h0_NeSmall_res : dataset_res option ;
ha_PC_res : dataset_res option ;
ha_PCOC_res : dataset_res option ;
ha_PC_NeBig_res : dataset_res option ;
ha_PC_NeSmall_res : dataset_res option ;
h0_NeBigInSmall_res : dataset_res option ;
h0_NeSmallInBig_res : dataset_res option ;
ha_PC_NeBigInSmall_res : dataset_res option ;
ha_PC_NeSmallInBig_res : dataset_res option ;
h0_NeG1_res : dataset_res option ;
h0_NeG2_res : dataset_res option ;
h0_NeG3_res : dataset_res option ;
......@@ -197,32 +184,27 @@ type res_all_hyp = {
haPC_NeG3_res : dataset_res option ;
haPC_NeG4_res : dataset_res option ;
haPC_NeG5_res : dataset_res option ;
haPC_NeG5_NeC_div2_res : dataset_res option ;
haPC_NeG5_NeC_x2_res : dataset_res option ;
h0_NeG5_NeC_div2_res : dataset_res option ;
h0_NeG5_NeC_x2_res : dataset_res option ;
}
let make_t_choices_per_couple {h0_res; h0_NeBig_res; h0_NeSmall_res; ha_PC_res; ha_PCOC_res; ha_PC_NeBig_res ; ha_PC_NeSmall_res;
h0_NeBigInSmall_res; h0_NeSmallInBig_res; ha_PC_NeBigInSmall_res; ha_PC_NeSmallInBig_res;
let make_t_choices_per_couple {ha_PCOC_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_NeG5_NeC_div2_res;
haPC_NeG5_NeC_x2_res ;
h0_NeG5_NeC_div2_res ;
h0_NeG5_NeC_x2_res ;
} =
let h0_mr = get_merged_results_opt h0_res in
let h0_NeBig_mr = get_merged_results_opt h0_NeBig_res in
let h0_NeSmall_mr = get_merged_results_opt h0_NeSmall_res in
let h0_NeBigInSmall_mr = get_merged_results_opt h0_NeBigInSmall_res in
let h0_NeSmallInBig_mr = get_merged_results_opt h0_NeSmallInBig_res in
let haPCOC_mr = get_merged_results_opt ha_PCOC_res in
let haPC_mr = get_merged_results_opt ha_PC_res in
let haPC_NeBig_mr = get_merged_results_opt ha_PC_NeBig_res in
let haPC_NeSmall_mr = get_merged_results_opt ha_PC_NeSmall_res in
let haPC_NeBigInSmall_mr = get_merged_results_opt ha_PC_NeBigInSmall_res in
let haPC_NeSmallInBig_mr = get_merged_results_opt ha_PC_NeSmallInBig_res in
let h0_NeG1_mr = get_merged_results_opt h0_NeG1_res in
let h0_NeG2_mr = get_merged_results_opt h0_NeG2_res in
let h0_NeG3_mr = get_merged_results_opt h0_NeG3_res in
......@@ -233,9 +215,14 @@ let make_t_choices_per_couple {h0_res; h0_NeBig_res; h0_NeSmall_res; ha_PC_res;
let haPC_NeG3_mr = get_merged_results_opt haPC_NeG3_res in
let haPC_NeG4_mr = get_merged_results_opt haPC_NeG4_res in
let haPC_NeG5_mr = get_merged_results_opt haPC_NeG5_res in
let haPC_NeG5_NeC_div2_mr = get_merged_results_opt haPC_NeG5_NeC_div2_res in
let haPC_NeG5_NeC_x2_mr = get_merged_results_opt haPC_NeG5_NeC_x2_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
make_t_choices ~h0_mr ~h0_NeBig_mr ~h0_NeSmall_mr ~haPCOC_mr ~haPC_mr ~haPC_NeBig_mr ~haPC_NeSmall_mr ~h0_NeBigInSmall_mr
~h0_NeSmallInBig_mr ~haPC_NeBigInSmall_mr ~haPC_NeSmallInBig_mr ~h0_NeG1_mr
make_t_choices ~haPCOC_mr
~h0_NeG1_mr
~h0_NeG2_mr
~h0_NeG3_mr
~h0_NeG4_mr
......@@ -245,24 +232,17 @@ let make_t_choices_per_couple {h0_res; h0_NeBig_res; h0_NeSmall_res; ha_PC_res;
~haPC_NeG3_mr
~haPC_NeG4_mr
~haPC_NeG5_mr
~haPC_NeG5_NeC_div2_mr
~haPC_NeG5_NeC_x2_mr
~h0_NeG5_NeC_div2_mr
~h0_NeG5_NeC_x2_mr
()
let get_t_choices ~(dataset_results_l: dataset_res list) : t_choices option =
let h0_res = List.find dataset_results_l (is_hyp ~hyp: "H0" ) in
let h0_NeBig_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeBig" ) in
let h0_NeSmall_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeSmall" ) in
let h0_NeBigInSmall_res = List.find dataset_results_l (is_hyp ~hyp: "H0_BigNeInSmallNe") in
let h0_NeSmallInBig_res = List.find dataset_results_l (is_hyp ~hyp: "H0_SmallNeInBigNe") in
let ha_PCOC_res = List.find dataset_results_l (is_hyp ~hyp: "HaPCOC" ) in
let ha_PC_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC" ) in
let ha_PC_NeBig_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeBig" ) in
let ha_PC_NeSmall_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeSmall" ) in
let ha_PC_NeBigInSmall_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_BigNeInSmallNe") in
let ha_PC_NeSmallInBig_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_SmallNeInBigNe") in
let h0_NeG1_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG1" ) in
let h0_NeG2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG2" ) in
let h0_NeG3_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG3" ) in
......@@ -274,13 +254,18 @@ let get_t_choices ~(dataset_results_l: dataset_res list) : t_choices option =
let haPC_NeG4_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG4" ) in
let haPC_NeG5_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5" ) in
let haPC_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_div2" ) in
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
match (ha_PCOC_res) with
| ( Some ha_PCOC) ->
let t_choices_dir = make_t_choices_per_couple {h0_res; h0_NeBig_res; h0_NeSmall_res; ha_PC_res; ha_PCOC_res; ha_PC_NeBig_res ; ha_PC_NeSmall_res;
h0_NeBigInSmall_res; h0_NeSmallInBig_res; ha_PC_NeBigInSmall_res; ha_PC_NeSmallInBig_res ;
let t_choices_dir = make_t_choices_per_couple {ha_PCOC_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; } in
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} 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_complete = t_choices_dir / selector ["out.complete.tsv"] in
......
lib/scripts/calc_t_per_meth.R
View file @ 9f1d5072
......@@ -21,17 +21,12 @@ option_list = list(
make_option(c("--HaPC_NeG3" ) , type="character", default=NA, help="merged_results HaPC_NeG3" , metavar="character"),
make_option(c("--HaPC_NeG4" ) , type="character", default=NA, help="merged_results HaPC_NeG4" , metavar="character"),
make_option(c("--HaPC_NeG5" ) , type="character", default=NA, help="merged_results HaPC_NeG5" , metavar="character"),
make_option(c("--H0" ) , type="character", default=NA, help="merged_results H0" , metavar="character"),
make_option(c("--H0NeBig" ) , type="character", default=NA, help="merged_results H0NeBig" , metavar="character"),
make_option(c("--H0NeSmall" ) , type="character", default=NA, help="merged_results H0NeSmall" , metavar="character"),
make_option(c("--H0NeBigInSmall" ) , type="character", default=NA, help="merged_results H0NeBigInSmall" , metavar="character"),
make_option(c("--H0NeSmallInBig" ) , type="character", default=NA, help="merged_results H0NeSmallInBig" , metavar="character"),
make_option(c("--HaPC_NeG5_NeC_div2_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_NeC_div2_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_x2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_x2_res" , metavar="character"),
make_option(c("--HaPCOC" ) , type="character", default=NA, help="merged_results HaPCOC" , metavar="character"),
make_option(c("--HaPC" ) , type="character", default=NA, help="merged_results HaPC" , metavar="character"),
make_option(c("--HaPCNeBig" ) , type="character", default=NA, help="merged_results HaPCNeBig" , metavar="character"),
make_option(c("--HaPCNeSmall" ) , type="character", default=NA, help="merged_results HaPCNeSmall" , metavar="character"),
make_option(c("--HaPCNeBigInSmall") , type="character", default=NA, help="merged_results HaPCNeBigInSmall", metavar="character"),
make_option(c("--HaPCNeSmallInBig") , type="character", default=NA, help="merged_results HaPCNeSmallInBig", metavar="character"),
make_option(c("-o","--out"), type="character", default="out",
help="output prefix [default= %default]", metavar="character")
......@@ -42,7 +37,7 @@ opt = parse_args(opt_parser);
print(opt)
if (is.na(opt$H0) & is.na(opt$H0_NeG1)){
if (is.na(opt$H0_NeG1)){
print_help(opt_parser)
stop("At least one argument must be supplied (H0_NeG1 or H0 input file)", call.=FALSE)
}
......@@ -80,20 +75,16 @@ df_HaPC_NeG2_melt = read_hyp(opt$HaPC_NeG2 )
df_HaPC_NeG3_melt = read_hyp(opt$HaPC_NeG3 )
df_HaPC_NeG4_melt = read_hyp(opt$HaPC_NeG4 )
df_HaPC_NeG5_melt = read_hyp(opt$HaPC_NeG5 )
df_H0_melt = read_hyp(opt$H0)
df_H0NeBig_melt = read_hyp(opt$H0NeBig)
df_H0NeSmall_melt = read_hyp(opt$H0NeSmall)
df_H0NeBigInSmall_melt = read_hyp(opt$H0NeBigInSmall)
df_H0NeSmallInBig_melt = read_hyp(opt$H0NeSmallInBig)
df_HaPC_NeG5_NeC_div2_melt = read_hyp(opt$HaPC_NeG5_NeC_div2)
df_HaPC_NeG5_NeC_x2_melt = read_hyp(opt$HaPC_NeG5_NeC_x2 )
df_HaPC_NeG5_NeC_div2_melt = read_hyp(opt$H0_NeG5_NeC_div2 )
df_HaPC_NeG5_NeC_x2_melt = read_hyp(opt$H0_NeG5_NeC_x2 )
df_HaPCOC_melt = read_hyp(opt$HaPCOC)
print(df_HaPCOC_melt)
df_HaPC_melt = read_hyp(opt$HaPC)
print(df_HaPC_melt)
df_HaPCNeBig_melt = read_hyp(opt$HaPCNeBig)
df_HaPCNeSmall_melt = read_hyp(opt$HaPCNeSmall)
df_HaPCNeBigInSmall_melt = read_hyp(opt$HaPCNeBigInSmall)
df_HaPCNeSmallInBig_melt = read_hyp(opt$HaPCNeSmallInBig)
......@@ -121,22 +112,18 @@ df_d_H0HaPC_NeG3 = build_df_dist_couple(df_H0_NeG3_melt, df_HaPC_NeG3_melt, "H
df_d_H0HaPC_NeG4 = build_df_dist_couple(df_H0_NeG4_melt, df_HaPC_NeG4_melt, "H0/HaPC NeG4")
df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5_melt, df_HaPC_NeG5_melt, "H0/HaPC NeG5")
df_d_H0HaPC_NeG5_NeC_div2 = build_df_dist_couple(df_H0_NeG5_NeC_div2_melt, df_HaPC_NeG5_melt, "H0/HaPC NeG5_NeC_div2")
df_d_H0HaPC_NeG5_NeC_x2 = build_df_dist_couple(df_H0_NeG5_NeC_x2_melt, df_HaPC_NeG5_NeC_x2_melt, "H0/HaPC NeG5_NeC_x2")
df_d_H0HaPCOC = build_df_dist_couple(df_H0_melt, df_HaPCOC_melt, "H0/HaPCOC")
df_d_H0HaPC = build_df_dist_couple(df_H0_melt, df_HaPC_melt, "H0/HaPC")
df_d_H0HaPC_NeBig = build_df_dist_couple(df_H0NeBig_melt, df_HaPCNeBig_melt, "H0/HaPC NeBig")
df_d_H0HaPC_NeSmall = build_df_dist_couple(df_H0NeSmall_melt, df_HaPCNeSmall_melt, "H0/HaPC NeSmall")
df_d_H0HaPC_NeBigInSmall = build_df_dist_couple(df_H0NeBigInSmall_melt, df_HaPCNeBigInSmall_melt, "H0/HaPC NeBigInSmall")
df_d_H0HaPC_NeSmallInBig = build_df_dist_couple(df_H0NeSmallInBig_melt, df_HaPCNeSmallInBig_melt, "H0/HaPC NeSmallInBig")
df_d = rbind.data.frame(df_d_H0HaPC, df_d_H0HaPCOC,df_d_H0HaPC_NeBig,df_d_H0HaPC_NeSmall,
df_d_H0HaPC_NeBigInSmall,df_d_H0HaPC_NeSmallInBig,
df_d = rbind.data.frame(
df_d_H0HaPCOC_NeG1,
df_d_H0HaPC_NeG1,
df_d_H0HaPC_NeG2,
df_d_H0HaPC_NeG3,
df_d_H0HaPC_NeG4,
df_d_H0HaPC_NeG5)
df_d_H0HaPC_NeG5,
df_d_H0HaPC_NeG5_NeC_div2,
df_d_H0HaPC_NeG5_NeC_x2)
df_d = df_d[order(df_d$methode),]
......@@ -203,18 +190,12 @@ df_H0HaPC_NeG4 = build_df_couple(df_H0_NeG4_melt, df_HaPC_NeG4_melt, "H0/HaPC
df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5_melt, df_HaPC_NeG5_melt, "H0/HaPC NeG5")
df_H0HaPC_NeG5_NeC_div2 = build_df_couple(df_H0_NeG5_NeC_div2_melt, df_HaPC_NeG5_melt, "H0/HaPC NeG5_NeC_div2")
df_H0HaPC_NeG5_NeC_x2 = build_df_couple(df_H0_NeG5_NeC_x2_melt, df_HaPC_NeG5_NeC_x2_melt, "H0/HaPC NeG5_NeC_x2")
df_H0HaPC = build_df_couple(df_H0_melt, df_HaPC_melt, "H0/HaPC")
df_H0HaPC_NeBig = build_df_couple(df_H0NeBig_melt, df_HaPCNeBig_melt, "H0/HaPC NeBig")
df_H0HaPC_NeSmall = build_df_couple(df_H0NeSmall_melt, df_HaPCNeSmall_melt, "H0/HaPC NeSmall")
df_H0HaPC_NeBigInSmall = build_df_couple(df_H0NeBigInSmall_melt, df_HaPCNeBigInSmall_melt, "H0/HaPC NeBigInSmall")
df_H0HaPC_NeSmallInBig = build_df_couple(df_H0NeSmallInBig_melt, df_HaPCNeSmallInBig_melt, "H0/HaPC NeSmallInBig")
df_H0HaPCOC = build_df_couple(df_H0_melt, df_HaPCOC_melt, "H0/HaPCOC")
df_l = list(df_H0HaPC, df_H0HaPCOC,df_H0HaPC_NeBig,df_H0HaPC_NeSmall,
df_H0HaPC_NeBigInSmall,df_H0HaPC_NeSmallInBig,df_H0HaPCOC_NeG1,
df_H0HaPC_NeG1, df_H0HaPC_NeG2, df_H0HaPC_NeG3, df_H0HaPC_NeG4, df_H0HaPC_NeG5)
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_x2)
df_l = df_l[-which(sapply(df_l, is.null))]
df = do.call("rbind",df_l)
......
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