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VEBER Philippe
codepi
Commits
377f7f64
Commit
377f7f64
authored
Sep 07, 2018
by
Carine Rey
Committed by
LANORE Vincent
Sep 12, 2018
Browse files
Revert "try NeG5_NeC_2.5 et NeG2.5_NeC5"
This reverts commit
ed2857b1
.
parent
956fe71d
Changes
5
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5 changed files
with
83 additions
and
84 deletions
+83
-84
lib/convergence_hypothesis.ml
lib/convergence_hypothesis.ml
+12
-12
lib/pipeline.ml
lib/pipeline.ml
+16
-16
lib/post_analyses.ml
lib/post_analyses.ml
+29
-29
lib/scripts/calc_t_per_meth.R
lib/scripts/calc_t_per_meth.R
+22
-23
lib/tree_dataset.ml
lib/tree_dataset.ml
+4
-4
No files found.
lib/convergence_hypothesis.ml
View file @
377f7f64
...
...
@@ -18,10 +18,10 @@ type t =
|
HaPCOC
|
HaPC_NeG5_NeC_div2
|
HaPC_NeG5_NeC_x2
|
HaPC_NeG
2
_NeC_5
|
HaPC_NeG5_NeC_
2
|
H0_NeG
2
_NeC_5
|
H0_NeG5_NeC_
2
|
HaPC_NeG
1
_NeC_5
|
HaPC_NeG5_NeC_
1
|
H0_NeG
1
_NeC_5
|
H0_NeG5_NeC_
1
let
string_of_model
m
=
match
m
with
|
H0_NeG1
->
"H0_NeG1"
...
...
@@ -39,10 +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_NeG
2
_NeC_5
->
"HaPC_NeG
2
_NeC_5"
|
HaPC_NeG5_NeC_
2
->
"HaPC_NeG5_NeC_
2
"
|
H0_NeG
2
_NeC_5
->
"H0_NeG
2
_NeC_5"
|
H0_NeG5_NeC_
2
->
"H0_NeG5_NeC_
2
"
|
HaPC_NeG
1
_NeC_5
->
"HaPC_NeG
1
_NeC_5"
|
HaPC_NeG5_NeC_
1
->
"HaPC_NeG5_NeC_
1
"
|
H0_NeG
1
_NeC_5
->
"H0_NeG
1
_NeC_5"
|
H0_NeG5_NeC_
1
->
"H0_NeG5_NeC_
1
"
let
assign
k
v
=
seq
~
sep
:
"="
[
string
k
;
v
]
...
...
@@ -113,9 +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_NeG
2
_NeC_5
->
bpp_config_HaPC_F_Ne
|
HaPC_NeG5_NeC_
2
->
bpp_config_HaPC_F_Ne
|
H0_NeG
2
_NeC_5
->
bpp_config_H0_F_Ne
|
H0_NeG5_NeC_
2
->
bpp_config_H0_F_Ne
|
HaPC_NeG
1
_NeC_5
->
bpp_config_HaPC_F_Ne
|
HaPC_NeG5_NeC_
1
->
bpp_config_HaPC_F_Ne
|
H0_NeG
1
_NeC_5
->
bpp_config_H0_F_Ne
|
H0_NeG5_NeC_
1
->
bpp_config_H0_F_Ne
;
]
lib/pipeline.ml
View file @
377f7f64
...
...
@@ -77,10 +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_NeG
2
_NeC_5
->
2
.
5
|
HaPC_NeG5_NeC_
2
->
5
.
|
H0_NeG
2
_NeC_5
->
2
.
5
|
H0_NeG5_NeC_
2
->
5
.
|
HaPC_NeG
1
_NeC_5
->
1
.
|
HaPC_NeG5_NeC_
1
->
5
.
|
H0_NeG
1
_NeC_5
->
1
.
|
H0_NeG5_NeC_
1
->
5
.
|
_
->
1
.
in
let
ne_c
=
match
model
with
...
...
@@ -98,10 +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_NeG
2
_NeC_5
->
5
.
|
HaPC_NeG5_NeC_
2
->
2
.
5
|
H0_NeG
2
_NeC_5
->
5
.
|
H0_NeG5_NeC_
2
->
2
.
5
|
HaPC_NeG
1
_NeC_5
->
5
.
|
HaPC_NeG5_NeC_
1
->
1
.
|
H0_NeG
1
_NeC_5
->
5
.
|
H0_NeG5_NeC_
1
->
1
.
|
_
->
ne_g
in
let
ne_a
=
match
model
with
...
...
@@ -119,10 +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_NeG
2
_NeC_5
->
ne_g
|
HaPC_NeG5_NeC_
2
->
ne_g
|
H0_NeG
2
_NeC_5
->
ne_g
|
H0_NeG5_NeC_
2
->
ne_g
|
HaPC_NeG
1
_NeC_5
->
ne_g
|
HaPC_NeG5_NeC_
1
->
ne_g
|
H0_NeG
1
_NeC_5
->
ne_g
|
H0_NeG5_NeC_
1
->
ne_g
|
_
->
ne_g
in
let
profile_f
=
profile
.
profile_f
in
...
...
@@ -172,10 +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_NeG
2
_NeC_5
;
HaPC_NeG5_NeC_
2
;
H0_NeG
2
_NeC_5
;
H0_NeG5_NeC_
2
;
HaPC_NeG
1
_NeC_5
;
HaPC_NeG5_NeC_
1
;
H0_NeG
1
_NeC_5
;
H0_NeG5_NeC_
1
;
]
);
(
if
ne_test
then
...
...
lib/post_analyses.ml
View file @
377f7f64
...
...
@@ -70,10 +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_
2
_mr
~
haPC_NeG
2
_NeC_5_mr
~
h0_NeG
2
_NeC_5_mr
~
h0_NeG5_NeC_
2
_mr
~
haPC_NeG5_NeC_
1
_mr
~
haPC_NeG
1
_NeC_5_mr
~
h0_NeG
1
_NeC_5_mr
~
h0_NeG5_NeC_
1
_mr
~
haPC_NeG5_indel_mr
()
:
post_analyses_dir
directory
workflow
=
let
env
=
Env
.
env_r
in
...
...
@@ -93,10 +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_
2
_res"
,
haPC_NeG5_NeC_
2
_mr
);
(
"--H0_NeG5_NeC_
2
_res"
,
h0_NeG5_NeC_
2
_mr
);
(
"--HaPC_NeG
2
_NeC_5_res"
,
haPC_NeG
2
_NeC_5_mr
);
(
"--H0_NeG
2
_NeC_5_res"
,
h0_NeG
2
_NeC_5_mr
);
(
"--HaPC_NeG5_NeC_
1
_res"
,
haPC_NeG5_NeC_
1
_mr
);
(
"--H0_NeG5_NeC_
1
_res"
,
h0_NeG5_NeC_
1
_mr
);
(
"--HaPC_NeG
1
_NeC_5_res"
,
haPC_NeG
1
_NeC_5_mr
);
(
"--H0_NeG
1
_NeC_5_res"
,
h0_NeG
1
_NeC_5_mr
);
(
"--H0_NeG5_indel_res"
,
h0_NeG5_indel_mr
);
(
"--HaPC_NeG5_indel_res"
,
haPC_NeG5_indel_mr
);
(
"--HaPCOC"
,
haPCOC_mr
);
...
...
@@ -201,10 +201,10 @@ type res_all_hyp = {
h0_NeG5_NeC_div2_res
:
dataset_res
option
;
h0_NeG5_NeC_x2_res
:
dataset_res
option
;
haPC_NeG5_NeC_
2
_res
:
dataset_res
option
;
haPC_NeG
2
_NeC_5_res
:
dataset_res
option
;
h0_NeG5_NeC_
2
_res
:
dataset_res
option
;
h0_NeG
2
_NeC_5_res
:
dataset_res
option
;
haPC_NeG5_NeC_
1
_res
:
dataset_res
option
;
haPC_NeG
1
_NeC_5_res
:
dataset_res
option
;
h0_NeG5_NeC_
1
_res
:
dataset_res
option
;
h0_NeG
1
_NeC_5_res
:
dataset_res
option
;
h0_NeG5_indel_res
:
dataset_res
option
;
haPC_NeG5_indel_res
:
dataset_res
option
;
...
...
@@ -221,10 +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_
2
_res
;
haPC_NeG
2
_NeC_5_res
;
h0_NeG5_NeC_
2
_res
;
h0_NeG
2
_NeC_5_res
;
haPC_NeG5_NeC_
1
_res
;
haPC_NeG
1
_NeC_5_res
;
h0_NeG5_NeC_
1
_res
;
h0_NeG
1
_NeC_5_res
;
h0_NeG5_indel_res
;
haPC_NeG5_indel_res
;
}
=
...
...
@@ -247,10 +247,10 @@ 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_
2
_mr
=
get_merged_results_opt
haPC_NeG5_NeC_
2
_res
in
let
haPC_NeG
2
_NeC_5_mr
=
get_merged_results_opt
haPC_NeG
2
_NeC_5_res
in
let
h0_NeG
2
_NeC_5_mr
=
get_merged_results_opt
h0_NeG
2
_NeC_5_res
in
let
h0_NeG5_NeC_
2
_mr
=
get_merged_results_opt
h0_NeG5_NeC_
2
_res
in
let
haPC_NeG5_NeC_
1
_mr
=
get_merged_results_opt
haPC_NeG5_NeC_
1
_res
in
let
haPC_NeG
1
_NeC_5_mr
=
get_merged_results_opt
haPC_NeG
1
_NeC_5_res
in
let
h0_NeG
1
_NeC_5_mr
=
get_merged_results_opt
h0_NeG
1
_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
...
...
@@ -272,10 +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_
2
_mr
~
haPC_NeG
2
_NeC_5_mr
~
h0_NeG
2
_NeC_5_mr
~
h0_NeG5_NeC_
2
_mr
~
haPC_NeG5_NeC_
1
_mr
~
haPC_NeG
1
_NeC_5_mr
~
h0_NeG
1
_NeC_5_mr
~
h0_NeG5_NeC_
1
_mr
()
...
...
@@ -299,10 +299,10 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
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_
2
_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_NeC_
2
"
)
in
let
haPC_NeG
2
_NeC_5_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG
2
_NeC_5"
)
in
let
h0_NeG5_NeC_
2
_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_NeC_
2
"
)
in
let
h0_NeG
2
_NeC_5_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG
2
_NeC_5"
)
in
let
haPC_NeG5_NeC_
1
_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_NeC_
1
"
)
in
let
haPC_NeG
1
_NeC_5_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG
1
_NeC_5"
)
in
let
h0_NeG5_NeC_
1
_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_NeC_
1
"
)
in
let
h0_NeG
1
_NeC_5_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG
1
_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
...
...
@@ -314,7 +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_
2
_res
;
haPC_NeG
2
_NeC_5_res
;
h0_NeG
2
_NeC_5_res
;
h0_NeG5_NeC_
2
_res
;
haPC_NeG5_NeC_
1
_res
;
haPC_NeG
1
_NeC_5_res
;
h0_NeG
1
_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 @
377f7f64
...
...
@@ -25,10 +25,10 @@ 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_
2
_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPC_NeG5_NeC_
2
_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG5_NeC_
2
_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG5_NeC_
2
_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--HaPC_NeG
2
_NeC_5_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPC_NeG
2
_NeC_5_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG
2
_NeC_5_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG
2
_NeC_5_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_NeG
1
_NeC_5_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPC_NeG
1
_NeC_5_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG
1
_NeC_5_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG
1
_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"
),
...
...
@@ -90,10 +90,10 @@ 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_
2
=
read_hyp
(
opt
$
HaPC_NeG5_NeC_
2
)
df_H0_NeG5_NeC_
2
=
read_hyp
(
opt
$
H0_NeG5_NeC_
2
)
df_HaPC_NeG
2
_NeC_5
=
read_hyp
(
opt
$
HaPC_NeG
2
_NeC_5
)
df_H0_NeG
2
_NeC_5
=
read_hyp
(
opt
$
H0_NeG
2
_NeC_5
)
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_NeG
1
_NeC_5
=
read_hyp
(
opt
$
HaPC_NeG
1
_NeC_5
)
df_H0_NeG
1
_NeC_5
=
read_hyp
(
opt
$
H0_NeG
1
_NeC_5
)
df_HaPC_NeG5_indel
=
read_hyp
(
opt
$
HaPC_NeG5_indel_res
)
df_H0_NeG5_indel
=
read_hyp
(
opt
$
H0_NeG5_indel_res
)
...
...
@@ -113,7 +113,6 @@ build_df_dist_couple = function (df_h0,df_ha,name) {
id_vars
=
if
(
"P_JSD"
%in%
colnames
(
df_h0
))
{
c
(
"Sites"
,
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
)}
else
{
c
(
"Sites"
)}
df_h0
=
melt
(
df_h0
,
id.vars
=
id_vars
,
variable.name
=
"methode"
)
df_ha
=
melt
(
df_ha
,
id.vars
=
id_vars
,
variable.name
=
"methode"
)
print
(
name
)
print
(
head
(
df_h0
))
df
=
merge
(
df_h0
,
df_ha
,
by
=
c
(
id_vars
,
"methode"
),
suffix
=
c
(
"_H0"
,
"_Ha"
))
df_melt
=
melt
(
df
,
id.vars
=
c
(
id_vars
,
"methode"
),
variable.name
=
"val_H0Ha"
)
...
...
@@ -134,8 +133,8 @@ 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_
2
=
build_df_dist_couple
(
df_H0_NeG5_NeC_
2
,
df_HaPC_NeG5_NeC_
2
,
"H0/HaPC NeG5_NeC_
2
"
)
df_d_H0HaPC_NeG
2
_NeC_5
=
build_df_dist_couple
(
df_H0_NeG
2
_NeC_5
,
df_HaPC_NeG
2
_NeC_5
,
"H0/HaPC NeG
2
_NeC_5"
)
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_NeG
1
_NeC_5
=
build_df_dist_couple
(
df_H0_NeG
1
_NeC_5
,
df_HaPC_NeG
1
_NeC_5
,
"H0/HaPC NeG
1
_NeC_5"
)
df_d_H0HaPC_NeG5_indel
=
build_df_dist_couple
(
df_H0_NeG5_indel
,
df_HaPC_NeG5_indel
,
"H0/HaPC NeG5_indel"
)
...
...
@@ -148,8 +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_
2
,
df_d_H0HaPC_NeG
2
_NeC_5
,
df_d_H0HaPC_NeG5_NeC_
1
,
df_d_H0HaPC_NeG
1
_NeC_5
,
df_d_H0HaPC_NeG5_indel
)
...
...
@@ -228,15 +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_
2
=
build_df_couple
(
df_H0_NeG5_NeC_
2
,
df_HaPC_NeG5_NeC_
2
,
"H0/HaPC NeG5_NeC_
2
"
)
df_H0HaPC_NeG
2
_NeC_5
=
build_df_couple
(
df_H0_NeG
2
_NeC_5
,
df_HaPC_NeG
2
_NeC_5
,
"H0/HaPC NeG
2
_NeC_5"
)
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_NeG
1
_NeC_5
=
build_df_couple
(
df_H0_NeG
1
_NeC_5
,
df_HaPC_NeG
1
_NeC_5
,
"H0/HaPC NeG
1
_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_
2
,
df_H0HaPC_NeG
2
_NeC_5
,
df_H0HaPC_NeG5_NeC_
1
,
df_H0HaPC_NeG
1
_NeC_5
,
df_H0HaPC_NeG5_NeC_x2
,
df_H0HaPC_NeG5_indel
)
df_l
=
df_l
[
-
which
(
sapply
(
df_l
,
is.null
))]
...
...
@@ -501,6 +500,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
print
(
head
(
df_out_melt2
))
df_out_melt2_dcast
=
dcast
(
df_out_melt2
,
methode
+
threshold
~
couple
,
value.var
=
"FPR"
)
print
(
head
(
df_out_melt2_dcast
))
print
(
df_out_melt2_dcast
)
# complete values for not existing threshold between couple
...
...
@@ -532,10 +532,13 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
df_out_melt2_dcast
$
H0NeG5
=
complete_value
(
df_out_melt2_dcast
,
"H0NeG5"
)
df_out_melt2_dcast
$
H0NeG5_NeC_x2
=
complete_value
(
df_out_melt2_dcast
,
"H0NeG5_NeC_x2"
)
df_out_melt2_dcast
$
H0NeG5_NeC_div2
=
complete_value
(
df_out_melt2_dcast
,
"H0NeG5_NeC_div2"
)
print
(
df_out_melt2_dcast
)
df_out_melt2_dcast
$
d_H0NeG5_NeC_x2_H0NeG5
=
df_out_melt2_dcast
$
H0NeG5_NeC_x2
-
df_out_melt2_dcast
$
H0NeG5
df_out_melt2_dcast
$
d_H0NeG5_NeC_div2_H0NeG5
=
df_out_melt2_dcast
$
H0NeG5_NeC_div2
-
df_out_melt2_dcast
$
H0NeG5
print
(
df_out_melt2_dcast
)
df_out_melt2_dcast_melt
=
melt
(
df_out_melt2_dcast
[,
c
(
"methode"
,
"threshold"
,
"d_H0NeG5_NeC_x2_H0NeG5"
,
"d_H0NeG5_NeC_div2_H0NeG5"
)],
id.vars
=
c
(
"methode"
,
"threshold"
))
print
(
head
(
df_out_melt2_dcast_melt
))
...
...
@@ -604,13 +607,13 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
)
plot_value_JSD
=
NULL
if
(
all
(
c
(
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
)
%in%
colnames
(
df_d
))
&
(
length
(
meths
)
<=
9
)
){
if
(
all
(
c
(
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
)
%in%
colnames
(
df_d
))){
print
(
"plot value/distance"
)
plot
=
ggplot
(
subset
(
df_d
,
val_H0Ha
==
"value_Ha"
)
,
aes
(
y
=
P_JSD
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
ggplot
(
df_d
,
aes
(
y
=
P_JSD
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"P JSD"
,
x
=
"Value"
)
...
...
@@ -624,11 +627,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_value_JSD
=
plot
print
(
head
(
df_d
))
print
(
table
(
df_d
$
val_H0Ha
,
df_d
$
methode
,
df_d
$
couple
))
plot
=
ggplot
(
subset
(
df_d
,
val_H0Ha
==
"value_Ha"
),
aes
(
y
=
P_ED
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
ggplot
(
df_d
,
aes
(
y
=
P_ED
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"P ED"
,
x
=
"Value"
)
...
...
lib/tree_dataset.ml
View file @
377f7f64
...
...
@@ -32,10 +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_NeG
2
_NeC_5
->
[
"tree.Ha.node_ids"
]
|
HaPC_NeG5_NeC_
2
->
[
"tree.Ha.node_ids"
]
|
H0_NeG
2
_NeC_5
->
[
"tree.H0_a.node_ids"
]
|
H0_NeG5_NeC_
2
->
[
"tree.H0_a.node_ids"
]
|
HaPC_NeG
1
_NeC_5
->
[
"tree.Ha.node_ids"
]
|
HaPC_NeG5_NeC_
1
->
[
"tree.Ha.node_ids"
]
|
H0_NeG
1
_NeC_5
->
[
"tree.H0_a.node_ids"
]
|
H0_NeG5_NeC_
1
->
[
"tree.H0_a.node_ids"
]
)
let
tree
dataset
mode
=
...
...
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