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VEBER Philippe
codepi
Commits
b8f7e2e2
Commit
b8f7e2e2
authored
Sep 07, 2018
by
Carine Rey
Browse files
add auc in output but still some pbs with identical
parent
ef8b0a4b
Changes
5
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Showing
5 changed files
with
15 additions
and
11 deletions
+15
-11
etc/docker/r_basics/Dockerfile
etc/docker/r_basics/Dockerfile
+3
-0
etc/docker/r_basics/build_docker.sh
etc/docker/r_basics/build_docker.sh
+1
-1
lib/env.ml
lib/env.ml
+1
-1
lib/post_analyses.ml
lib/post_analyses.ml
+3
-3
lib/scripts/calc_t_per_meth.R
lib/scripts/calc_t_per_meth.R
+7
-6
No files found.
etc/docker/r_basics/Dockerfile
View file @
b8f7e2e2
...
@@ -11,3 +11,6 @@ RUN apt-get update && \
...
@@ -11,3 +11,6 @@ RUN apt-get update && \
RUN
echo
'source("https://bioconductor.org/biocLite.R"); biocLite("ggtree")'
>
/tmp/packages.R
\
RUN
echo
'source("https://bioconductor.org/biocLite.R"); biocLite("ggtree")'
>
/tmp/packages.R
\
&&
Rscript /tmp/packages.R
&&
Rscript /tmp/packages.R
RUN
echo
'install.packages("flux")'
>
/tmp/packages.R
\
&&
Rscript /tmp/packages.R
etc/docker/r_basics/build_docker.sh
View file @
b8f7e2e2
...
@@ -4,7 +4,7 @@ set -e
...
@@ -4,7 +4,7 @@ set -e
IMAGE_NAME
=
r_basics
IMAGE_NAME
=
r_basics
DOCKERFILE_DIR
=
.
DOCKERFILE_DIR
=
.
TAG
=
0
801
2018
TAG
=
0
907
2018
REPO
=
carinerey/
$IMAGE_NAME
:
$TAG
REPO
=
carinerey/
$IMAGE_NAME
:
$TAG
docker build
-t
$REPO
-f
./Dockerfile
$DOCKERFILE_DIR
docker build
-t
$REPO
-f
./Dockerfile
$DOCKERFILE_DIR
...
...
lib/env.ml
View file @
b8f7e2e2
...
@@ -8,7 +8,7 @@ let env_tdg09 = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1.
...
@@ -8,7 +8,7 @@ let env_tdg09 = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1.
let
env_py
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
let
env_py
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
let
env_r
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"0
801
2018"
()
let
env_r
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"0
907
2018"
()
let
env_phyml
=
docker_image
~
account
:
"carinerey"
~
name
:
"phyml"
~
tag
:
"v3.1"
()
let
env_phyml
=
docker_image
~
account
:
"carinerey"
~
name
:
"phyml"
~
tag
:
"v3.1"
()
...
...
lib/post_analyses.ml
View file @
b8f7e2e2
...
@@ -340,8 +340,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
...
@@ -340,8 +340,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let
haPC_NeG5_indel_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_0.33_i"
)
in
let
haPC_NeG5_indel_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_0.33_i"
)
in
match
(
h
a_PCOC
_res
)
with
match
(
h
0_NeG1
_res
)
with
|
(
Some
h
a_PCOC
)
->
|
(
Some
h
0_NeG1
)
->
let
t_choices_dir
=
make_t_choices_per_couple
~
tree_prefix
{
ha_PCOC_res
;
let
t_choices_dir
=
make_t_choices_per_couple
~
tree_prefix
{
ha_PCOC_res
;
h0_NeG1_res
;
h0_NeG2_res
;
h0_NeG3_res
;
h0_NeG4_res
;
h0_NeG5_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_NeG1_res
;
haPC_NeG2_res
;
haPC_NeG3_res
;
haPC_NeG4_res
;
haPC_NeG5_res
;
...
@@ -357,7 +357,7 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
...
@@ -357,7 +357,7 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let
t_choices_condensed_plot_png
=
t_choices_dir
/
selector
[
"out_condensed.png"
]
in
let
t_choices_condensed_plot_png
=
t_choices_dir
/
selector
[
"out_condensed.png"
]
in
let
rp_plot
=
t_choices_dir
/
selector
[
"out_condensed.recall_precision_ok.pdf"
]
in
let
rp_plot
=
t_choices_dir
/
selector
[
"out_condensed.recall_precision_ok.pdf"
]
in
let
auc_tsv
=
t_choices_dir
/
selector
[
"out.auc_condensed.tsv"
]
in
let
auc_tsv
=
t_choices_dir
/
selector
[
"out.auc_condensed.tsv"
]
in
let
tree_prefix
=
h
a_PCOC
.
tree_prefix
in
let
tree_prefix
=
h
0_NeG1
.
tree_prefix
in
Some
{
t_choices_max
;
t_choices_recall09
;
t_choices_complete
;
t_choices_plot
;
t_choices_condensed_plot
;
t_choices_condensed_plot_png
;
rp_plot
;
auc_tsv
;
tree_prefix
}
Some
{
t_choices_max
;
t_choices_recall09
;
t_choices_complete
;
t_choices_plot
;
t_choices_condensed_plot
;
t_choices_condensed_plot_png
;
rp_plot
;
auc_tsv
;
tree_prefix
}
|
_
->
None
|
_
->
None
...
...
lib/scripts/calc_t_per_meth.R
View file @
b8f7e2e2
...
@@ -174,8 +174,8 @@ df_d = rbind.data.frame(
...
@@ -174,8 +174,8 @@ df_d = rbind.data.frame(
df_d_H0H0_NeG5NeG5_NeC1
,
df_d_H0H0_NeG5NeG5_NeC1
,
df_d_H0HaPC_NeG4_NeC_1
,
df_d_H0HaPC_NeG4_NeC_1
,
df_d_H0HaPC_NeG1_NeC_4
,
df_d_H0HaPC_NeG1_NeC_4
,
df_d_H0H0_NeG4NeG4_NeC
2
,
df_d_H0H0_NeG4NeG4_NeC
1
,
df_d_H0H0_NeG
2
NeG
2
_NeC4
,
df_d_H0H0_NeG
1
NeG
1
_NeC4
,
df_d_H0HaPC_NeG5_indel
df_d_H0HaPC_NeG5_indel
)
)
...
@@ -366,9 +366,10 @@ df_auc = do.call(rbind, lapply(split(df_out,paste0(df_out$methode,df_out$couple)
...
@@ -366,9 +366,10 @@ df_auc = do.call(rbind, lapply(split(df_out,paste0(df_out$methode,df_out$couple)
P
=
x
$
precision98_02
P
=
x
$
precision98_02
R
=
R
[
!
is.na
(
P
)]
R
=
R
[
!
is.na
(
P
)]
P
=
P
[
!
is.na
(
P
)]
P
=
P
[
!
is.na
(
P
)]
print
(
R
)
auc
=
0
print
(
P
)
if
(
length
(
P
)
>
1
)
{
auc
=
auc
(
x
=
R
,
y
=
P
,
dens
=
0
)
auc
=
auc
(
x
=
R
,
y
=
P
,
dens
=
1
)
}
df
=
data.frame
(
methode
=
x
$
methode
[
1
]
,
couple
=
x
$
couple
[
1
]
,
auc
=
auc
)
df
=
data.frame
(
methode
=
x
$
methode
[
1
]
,
couple
=
x
$
couple
[
1
]
,
auc
=
auc
)
return
(
df
)
return
(
df
)
}))
}))
...
@@ -499,7 +500,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
...
@@ -499,7 +500,7 @@ 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
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot
}
plot
}
plot
=
plot_PR_c
(
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG2"
,
"H0/HaPC NeG4"
,
"H0/H0 NeG4/NeG4_NeC_1"
,
"H0/H0 NeG1/NeG1_NeC_4"
,
"H0/HaPC NeG4_NeC_1"
,
"H0/HaPC NeG1_NeC_4"
)
plot
=
plot_PR_c
(
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG2"
,
"H0/HaPC NeG4"
,
"H0/H0 NeG4/NeG4_NeC_1"
,
"H0/H0 NeG1/NeG1_NeC_4"
,
"H0/HaPC NeG4_NeC_1"
,
"H0/HaPC NeG1_NeC_4"
)
)
plot1
=
plot_PR_c
(
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG2"
,
"H0/HaPC NeG4"
))
plot1
=
plot_PR_c
(
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG2"
,
"H0/HaPC NeG4"
))
plot2
=
plot_PR_c
(
c
(
"H0/H0 NeG4/NeG4_NeC_1"
,
"H0/H0 NeG1/NeG1_NeC_4"
,
"NULL"
))
plot2
=
plot_PR_c
(
c
(
"H0/H0 NeG4/NeG4_NeC_1"
,
"H0/H0 NeG1/NeG1_NeC_4"
,
"NULL"
))
plot3
=
plot_PR_c
(
c
(
"H0/HaPC NeG4_NeC_1"
,
"H0/HaPC NeG1_NeC_4"
,
"NULL"
))
plot3
=
plot_PR_c
(
c
(
"H0/HaPC NeG4_NeC_1"
,
"H0/HaPC NeG1_NeC_4"
,
"NULL"
))
...
...
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