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VEBER Philippe
codepi
Commits
7cfa4b5b
Commit
7cfa4b5b
authored
Sep 26, 2018
by
Carine Rey
Browse files
prep figures
parent
1a767716
Changes
2
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Showing
2 changed files
with
17 additions
and
17 deletions
+17
-17
lib/pipeline.ml
lib/pipeline.ml
+1
-1
lib/scripts/calc_t_per_meth.R
lib/scripts/calc_t_per_meth.R
+16
-16
No files found.
lib/pipeline.ml
View file @
7cfa4b5b
...
...
@@ -92,7 +92,7 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
[
Fixed
4
.
]
@
if
preview
then
[
Variable
(
8
.,
1
.
)]
else
[
Fixed
1
.;
Fixed
8
.;
(* 4->8, 8->4, 8, 16, 1->8 and 16->1 are new ; it means 6*2*2 tasks on cyp/C4A *)
Variable
(
1
.,
4
.
);
Variable
(
4
.,
1
.
);
Variable
(
4
.,
8
.
);
Variable
(
8
.,
1
.
);
Variable
(
4
.,
8
.
);
]
in
let
models
=
h0_hapc_forall
nes_list
in
...
...
lib/scripts/calc_t_per_meth.R
View file @
7cfa4b5b
...
...
@@ -681,9 +681,9 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
print
(
"plot recall_precision"
)
couple_plot1
=
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG4"
,
"H0/HaPC NeG8"
)
couple_plot2
=
c
(
"H0/H0 NeG1/NeG1_NeC_4"
,
"H0/H0 NeG4/NeG4_NeC_8"
,
"H0/H0 NeG
8
/NeG
8
_NeC_1"
)
couple_plot3
=
c
(
"H0/HaPC NeG1_NeC_4"
,
"H0/HaPC NeG4_NeC_8"
,
"H0/HaPC NeG
8
_NeC_1"
)
couple_plot4
=
c
(
"H0 NeG1/HaPC NeG1_NeC_4"
,
"H0 NeG4/HaPC NeG4_NeC_8"
,
"H0 NeG
8
/HaPC NeG
8
_NeC_1"
)
couple_plot2
=
c
(
"H0/H0 NeG1/NeG1_NeC_4"
,
"H0/H0 NeG4/NeG4_NeC_8"
,
"H0/H0 NeG
4
/NeG
4
_NeC_1"
)
couple_plot3
=
c
(
"H0/HaPC NeG1_NeC_4"
,
"H0/HaPC NeG4_NeC_8"
,
"H0/HaPC NeG
4
_NeC_1"
)
couple_plot4
=
c
(
"H0 NeG1/HaPC NeG1_NeC_4"
,
"H0 NeG4/HaPC NeG4_NeC_8"
,
"H0 NeG
4
/HaPC NeG
4
_NeC_1"
)
couple_i
=
c
(
couple_plot1
,
couple_plot2
,
couple_plot3
,
couple_plot4
)
...
...
@@ -737,7 +737,6 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot_PR_c
=
function
(
couple_l
)
{
if
(
sum
(
couple_l
%in%
df_out
$
couple
)
>
0
)
{
print
(
"PAS OK"
)
tmp_df
=
subset
(
df_out
,
couple
%in%
couple_l
)
tmp_df
$
couple
=
factor
(
tmp_df
$
couple
,
levels
=
c
(
levels
(
tmp_df
$
couple
),
"to_be_rm"
,
"to_be_rm2"
,
"to_be_rm3"
,
"to_be_rm4"
))
...
...
@@ -765,11 +764,12 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
from_c
=
c
(
couple_plot1
,
couple_plot2
,
couple_plot3
,
couple_plot4
)
couple_plot1_to
=
c
(
"PC NeS 1"
,
"PC NeS 4"
,
"PC NeS 8"
)
couple_plot2_to
=
c
(
"CCSE NeSA1 NeSC 4"
,
"CCSE NeSA4 NeSC 8"
,
"CCSE NeSA8 NeSC 1"
)
couple_plot3_to
=
c
(
"PC & GCSE NeSA1 NeSC 4"
,
"PC & GCSE NeSA4 NeSC 8"
,
"PC & GCSE NeSA
8
NeSC 1"
)
couple_plot4_to
=
c
(
"PC & CCSE NeSA1 NeSC 4"
,
"PC & CCSE NeSA4 NeSC 8"
,
"PC & CCSE NeSA
8
NeSC 1"
)
couple_plot3_to
=
c
(
"PC & GCSE NeSA1 NeSC 4"
,
"PC & GCSE NeSA4 NeSC 8"
,
"PC & GCSE NeSA
4
NeSC 1"
)
couple_plot4_to
=
c
(
"PC & CCSE NeSA1 NeSC 4"
,
"PC & CCSE NeSA4 NeSC 8"
,
"PC & CCSE NeSA
4
NeSC 1"
)
to_c
=
c
(
couple_plot1_to
,
couple_plot2_to
,
couple_plot3_to
,
couple_plot4_to
)
tmp_df
$
coupleF
=
mapvalues
(
tmp_df
$
couple
,
from
=
from_c
,
to
=
to_c
)
tmp_df
$
coupleF
=
factor
(
tmp_df
$
coupleF
,
levels
=
unique
(
c
(
couple_plot1_to
,
couple_plot2_to
,
couple_plot4_to
,
couple_plot3_to
)))
tmp_df
$
coupleF
=
factor
(
tmp_df
$
coupleF
,
levels
=
c
(
levels
(
tmp_df
$
coupleF
),
"to_be_rm"
,
"to_be_rm2"
,
"to_be_rm3"
,
"to_be_rm4"
))
plot
=
ggplot
(
tmp_df
,
aes
(
x
=
sensitivity
,
y
=
precision98_02
,
col
=
methode
))
plot
=
plot
+
theme_bw
()
...
...
@@ -820,9 +820,9 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
couple_simuA
=
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG4"
,
"H0/HaPC NeG8"
)
couple_simuB
=
c
(
"H0/H0 NeG1/NeG1_NeC_4"
,
"H0/H0 NeG4/NeG4_NeC_8"
,
"H0/H0 NeG
8
/NeG
8
_NeC_1"
)
couple_simuC
=
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG
8
_NeC_1"
,
"H0/HaPC NeG4"
,
"H0/HaPC NeG1_NeC_4"
,
"H0/HaPC NeG8"
,
"H0/HaPC NeG4_NeC_8"
)
couple_simuD
=
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG4"
,
"H0/HaPC NeG8"
,
"H0 NeG1/HaPC NeG1_NeC_4"
,
"H0 NeG4/HaPC NeG4_NeC_8"
,
"H0 NeG
8
/HaPC NeG
8
_NeC_1"
)
couple_simuB
=
c
(
"H0/H0 NeG1/NeG1_NeC_4"
,
"H0/H0 NeG4/NeG4_NeC_8"
,
"H0/H0 NeG
4
/NeG
4
_NeC_1"
)
couple_simuC
=
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG
4
_NeC_1"
,
"H0/HaPC NeG4"
,
"H0/HaPC NeG1_NeC_4"
,
"H0/HaPC NeG8"
,
"H0/HaPC NeG4_NeC_8"
)
couple_simuD
=
c
(
"H0/HaPC NeG1"
,
"H0/HaPC NeG4"
,
"H0/HaPC NeG8"
,
"H0 NeG1/HaPC NeG1_NeC_4"
,
"H0 NeG4/HaPC NeG4_NeC_8"
,
"H0 NeG
4
/HaPC NeG
4
_NeC_1"
)
tmp_df
$
group
[
tmp_df
$
couple
%in%
couple_simuA
]
=
"PC"
...
...
@@ -849,12 +849,12 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
from_c
=
c
(
couple_plot1
,
couple_plot2
,
couple_plot3
,
couple_plot4
)
couple_plot1_to
=
c
(
"NeS 1"
,
"NeS 4"
,
"NeS 8"
)
couple_plot2_to
=
c
(
"NeSA 1\nNeSC 4"
,
"NeSA 4\nNeSC 8"
,
"NeSA
8
\nNeSC 1"
)
couple_plot3_to
=
c
(
"NeSA 1\nNeSC 4"
,
"NeSA 4\nNeSC 8"
,
"NeSA
8
\nNeSC 1"
)
couple_plot4_to
=
c
(
"NeSA 1\nNeSC 4"
,
"NeSA 4\nNeSC 8"
,
"NeSA
8
\nNeSC 1"
)
couple_plot2_to
=
c
(
"NeSA 1\nNeSC 4"
,
"NeSA 4\nNeSC 8"
,
"NeSA
4
\nNeSC 1"
)
couple_plot3_to
=
c
(
"NeSA 1\nNeSC 4"
,
"NeSA 4\nNeSC 8"
,
"NeSA
4
\nNeSC 1"
)
couple_plot4_to
=
c
(
"NeSA 1\nNeSC 4"
,
"NeSA 4\nNeSC 8"
,
"NeSA
4
\nNeSC 1"
)
to_c
=
c
(
couple_plot1_to
,
couple_plot2_to
,
couple_plot3_to
,
couple_plot4_to
)
tmp_df
$
coupleX
=
mapvalues
(
tmp_df
$
couple
,
from
=
from_c
,
to
=
to_c
)
tmp_df
$
coupleX
=
factor
(
tmp_df
$
coupleX
,
levels
=
c
(
"NeS 1"
,
"NeSA
8
\nNeSC 1"
,
"NeS 4"
,
"NeSA 1\nNeSC 4"
,
"NeS 8"
,
"NeSA 4\nNeSC 8"
))
tmp_df
$
coupleX
=
factor
(
tmp_df
$
coupleX
,
levels
=
c
(
"NeS 1"
,
"NeSA
4
\nNeSC 1"
,
"NeS 4"
,
"NeSA 1\nNeSC 4"
,
"NeS 8"
,
"NeSA 4\nNeSC 8"
))
from_m
=
c
(
"PCOC"
,
"Mutinomial_1MinusLRT"
,
"Msd_0.05_1MinusP"
,
"Identical_LG08"
,
"Tdg09_1MinusLRT"
,
"Topological_LG08"
,
"Diffsel_mean"
)
to_m
=
c
(
"PCOC"
,
"Mutinomial"
,
"msd"
,
"Identical"
,
"TDG09"
,
"Topological"
,
"diffsel"
)
...
...
@@ -866,7 +866,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot
=
plot
+
labs
(
x
=
""
,
y
=
"AUC"
)
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
ylim
(
c
(
0
,
1
))
plot
=
plot
+
guides
(
fill
=
FALSE
)
#
plot = plot + guides(fill=FALSE)
plot
=
plot
+
scale_color_manual
(
values
=
colors2
)
plot
=
plot
+
scale_fill_manual
(
values
=
colors2
)
#plot = plot + geom_point(size=1, alpha=alpha)
...
...
@@ -911,7 +911,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot
=
plot
+
labs
(
x
=
""
,
y
=
"Recall at 90% of precision"
)
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
ylim
(
c
(
0
,
1
))
plot
=
plot
+
guides
(
fill
=
FALSE
)
#
plot = plot + guides(fill=FALSE)
plot
=
plot
+
scale_color_manual
(
values
=
colors2
)
#plot = plot + geom_point(size=1, alpha=alpha)
plot
=
plot
+
geom_point
(
na.rm
=
TRUE
,
position
=
position_dodge
(
width
=
0.5
),
size
=
1.5
,
alpha
=
1
)
...
...
@@ -922,7 +922,7 @@ plot_out = function(df_out, df_d , df_auc, df_recall_sup09_per_meth, meths = NUL
plot
=
plot_PR_c
(
couple_i
)
plot1
=
plot_PR_c
(
couple_plot1
)
plot1
=
plot_PR_c
(
c
(
"H0/HaPC NeG4"
,
"NULL2"
,
"NULL"
))
plot1
=
plot_PR_c
(
c
(
"
NULL"
,
"
H0/HaPC NeG4"
,
"NULL2"
))
plot2
=
plot_PR_c
(
couple_plot2
)
plot3
=
plot_PR_c
(
couple_plot3
)
plot4
=
plot_PR_c
(
couple_plot4
)
...
...
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