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VEBER Philippe
codepi
Commits
e67ee873
Commit
e67ee873
authored
Aug 31, 2018
by
Carine Rey
Browse files
fix errors if external usage
parent
6bce0845
Changes
1
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Showing
1 changed file
with
107 additions
and
105 deletions
+107
-105
lib/scripts/calc_t_per_meth.R
lib/scripts/calc_t_per_meth.R
+107
-105
No files found.
lib/scripts/calc_t_per_meth.R
View file @
e67ee873
...
...
@@ -26,7 +26,7 @@ option_list = list(
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
(
"--tree_prefix"
)
,
type
=
"character"
,
default
=
""
,
help
=
"tree_prefix"
,
metavar
=
"character"
),
...
...
@@ -99,10 +99,10 @@ build_df_dist_couple = function (df_h0,df_ha,name) {
if
((
!
is.null
(
df_h0
))
&
(
!
is.null
(
df_ha
)))
{
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"
)
df_ha
=
melt
(
df_ha
,
id.vars
=
id_vars
,
variable.name
=
"methode"
)
print
(
head
(
df_h0
))
df
=
merge
(
df_h0
,
df_ha
,
by
=
c
(
"Sites"
,
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
,
"methode"
),
suffix
=
c
(
"_H0"
,
"_Ha"
))
df_melt
=
melt
(
df
,
id.vars
=
c
(
"Sites"
,
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
,
"methode"
),
variable.name
=
"val_H0Ha"
)
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"
)
df_melt
$
couple
=
name
}
else
{
df_melt
=
NULL
...
...
@@ -167,7 +167,7 @@ calc_TN_FP_TP_FN = function(meth, df_H0, df_Ha){
t_list
=
c
(
0
,
1
,
df_H0
[,
meth
],
df_Ha
[,
meth
])
t_list
=
sort
(
t_list
)
t_list
=
unique
(
t_list
)
df_TN_FP
=
do.call
(
rbind.data.frame
,
lapply
(
t_list
,
calc_TN_FP
,
vals
=
df_H0
[,
meth
]))
df_TP_FN
=
do.call
(
rbind.data.frame
,
lapply
(
t_list
,
calc_TP_FN
,
vals
=
df_Ha
[,
meth
]))
...
...
@@ -181,7 +181,7 @@ calc_TN_FP_TP_FN = function(meth, df_H0, df_Ha){
build_df_couple
=
function
(
df_h0
,
df_ha
,
name
)
{
print
(
name
)
if
((
!
is.null
(
df_h0
))
&
(
!
is.null
(
df_ha
)))
{
id_vars
=
if
(
"P_JSD"
%in%
colnames
(
df_h0
))
{
c
(
"Sites"
,
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
)}
else
{
c
(
"Sites"
)}
id_vars
=
if
(
"P_JSD"
%in%
colnames
(
df_h0
))
{
c
(
"Sites"
,
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
)}
else
{
c
(
"Sites"
)}
meth_l
=
colnames
(
df_h0
)[
!
colnames
(
df_h0
)
%in%
id_vars
]
df
=
do.call
(
rbind.data.frame
,
lapply
(
unique
(
meth_l
)
,
calc_TN_FP_TP_FN
,
df_H0
=
df_h0
,
df_Ha
=
df_ha
))
df
$
couple
=
name
...
...
@@ -190,7 +190,7 @@ build_df_couple = function (df_h0,df_ha,name) {
df
=
NULL
print
(
df
)
}
return
(
df
)
}
...
...
@@ -349,7 +349,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
limitsize
=
FALSE
)
print
(
"plot recall_precision"
)
if
(
length
(
meths
)
<=
7
)
{
plot
=
ggplot
(
df_out
,
aes
(
x
=
sensitivity
,
y
=
precision98_02
,
col
=
methode
))
plot
=
plot
+
theme_bw
()
...
...
@@ -372,13 +372,13 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
colour
=
"black"
))
+
guides
(
colour
=
guide_legend
(
override.aes
=
list
(
alpha
=
1
,
size
=
3
),
nrow
=
2
))
)
plot_recall_precision_papier
=
plot_grid
(
legend_PR
,
plot
+
theme
(
legend.position
=
"none"
),
ncol
=
1
,
scale
=
1
,
labels
=
c
(
""
,
""
),
align
=
"h"
,
rel_heights
=
c
(
0.3
,
0.7
),
hjust
=
0
,
vjust
=
1
)
save_plot
(
paste0
(
opt
$
out
,
suffix
,
".recall_precision.pdf"
),
...
...
@@ -391,7 +391,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
}
else
{
plot_recall_precision_papier
=
NULL
}
print
(
"plot FPR"
)
#dcast
x_labs
=
"Threshold"
...
...
@@ -400,7 +400,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
df_out_melt2
$
couple
=
gsub
(
"/HaPC "
,
""
,
df_out_melt2
$
couple
)
df_out_melt2
=
subset
(
df_out_melt2
,
variable
==
"specificity"
)
df_out_melt2
$
FPR
=
1
-
df_out_melt2
$
value
if
(
length
(
df_out_melt2
$
methode
)
>
0
){
df_recall_sup09_per_meth2
=
subset
(
df_recall_sup09_per_meth
,
couple
%in%
c
(
"H0/HaPC NeG5"
,
"H0/HaPC NeG5_NeC_div2"
,
"H0/HaPC NeG5_NeC_x2"
))
df_recall_sup09_per_meth2
$
couple
=
gsub
(
"/HaPC "
,
""
,
df_recall_sup09_per_meth2
$
couple
)
...
...
@@ -428,21 +428,21 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
base_aspect_ratio
=
1.5
,
limitsize
=
FALSE
)
if
(
length
(
unique
(
df_out_melt2
$
couple
))
==
3
){
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
complete_value
=
function
(
df
,
col_name
)
{
print
(
colnames
(
df
))
print
(
col_name
)
df
=
df
[,
c
(
"methode"
,
"threshold"
,
col_name
)]
colnames
(
df
)
=
c
(
"methode"
,
"threshold"
,
"value"
)
fix_val
=
function
(
r
,
df_no_na
)
{
x
=
r
[
"value"
]
t
=
r
[
"threshold"
]
...
...
@@ -469,19 +469,19 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
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
))
df_out_melt2_dcast_melt
$
variable
=
factor
(
df_out_melt2_dcast_melt
$
variable
,
levels
=
c
(
"H0NeG5"
,
"H0NeG5_NeC_x2"
,
"H0NeG5_NeC_div2"
,
"d_H0NeG5_NeC_x2_H0NeG5"
,
"d_H0NeG5_NeC_div2_H0NeG5"
))
df_recall_sup09_per_meth3
=
subset
(
df_recall_sup09_per_meth2
,
couple
%in%
c
(
"H0NeG5"
))
df_recall_sup09_per_meth3
$
variable
=
df_recall_sup09_per_meth3
$
couple
df_recall_sup09_per_meth3
$
variable
=
factor
(
df_recall_sup09_per_meth3
$
variable
,
levels
=
c
(
"H0NeG5"
,
"H0NeG5_NeC_x2"
,
"H0NeG5_NeC_div2"
,
"d_H0NeG5_NeC_x2_H0NeG5"
,
"d_H0NeG5_NeC_div2_H0NeG5"
))
x_labs
=
"Threshold"
y_labs
=
"Delta FP Rate"
...
...
@@ -516,9 +516,8 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
plot
=
ggplot
(
df_out_melt
,
aes
(
x
=
threshold
,
y
=
value
,
col
=
couple
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
,
plot.margin
=
unit
(
x
=
c
(
0
,
0
,
0
,
0
),
units
=
"cm"
),
legend.background
=
element_rect
(
fill
=
"white"
,
size
=
0.5
,
linetype
=
"solid"
,
colour
=
"black"
))
+
guides
(
colour
=
guide_legend
(
override.aes
=
list
(
alpha
=
1
),
nrow
=
2
))
legend.background
=
element_rect
(
fill
=
"white"
,
size
=
0.5
,
linetype
=
"solid"
,
colour
=
"black"
))
+
guides
(
colour
=
guide_legend
(
override.aes
=
list
(
alpha
=
1
),
nrow
=
2
))
plot
=
plot
+
guides
(
fill
=
FALSE
)
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
x
=
x_labs
,
y
=
y_labs
)
#+ ylim(y_lim)
...
...
@@ -533,101 +532,104 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
plot_max_MCC
=
plot
save_plot
(
paste0
(
opt
$
out
,
suffix
,
".indicator_per_meth.pdf"
),
plot_max_MCC
,
ncol
=
0.4
*
length
(
unique
(
df_out_melt
$
methode
)),
nrow
=
1.7
,
base_aspect_ratio
=
1.5
,
limitsize
=
FALSE
)
plot_max_MCC
,
ncol
=
0.4
*
length
(
unique
(
df_out_melt
$
methode
)),
nrow
=
1.7
,
base_aspect_ratio
=
1.5
,
limitsize
=
FALSE
)
print
(
"plot value/distance"
)
if
(
all
((
df_out_melt
)
%in%
c
(
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
))){
print
(
"plot value/distance"
)
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"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
P_JSD
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_value_JSD
=
plot
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"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
P_ED
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_value_ED
=
plot
plot
=
ggplot
(
subset
(
df_d
,
val_H0Ha
==
"value_Ha"
),
aes
(
y
=
entropy_C2
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"Entropy C2"
,
x
=
"Value"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C2
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_entropy_C2
=
plot
plot
=
ggplot
(
df_d
,
aes
(
y
=
entropy_C1
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"Entropy C1"
,
x
=
"Value"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C2
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_entropy_C1
=
plot
plot
=
ggplot
(
subset
(
df_d
,
val_H0Ha
==
"value_Ha"
)
,
aes
(
y
=
entropy_C2
,
x
=
entropy_C1
,
shape
=
val_H0Ha
,
col
=
value
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"Entropy C2"
,
x
=
"Entropy C1"
)
plot
=
plot
+
xlim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C1
),
1
)))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C2
),
1
)))
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
scale_colour_gradientn
(
colours
=
c
(
"red"
,
"yellow"
,
"green"
,
"lightblue"
,
"darkblue"
),
values
=
c
(
1.0
,
0.8
,
0.6
,
0.4
,
0.2
,
0
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_entropy_C2_C1
=
plot
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"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
P_JSD
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_value_JSD
=
plot
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"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
P_ED
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_value_ED
=
plot
plot
=
ggplot
(
subset
(
df_d
,
val_H0Ha
==
"value_Ha"
),
aes
(
y
=
entropy_C2
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"Entropy C2"
,
x
=
"Value"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C2
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_entropy_C2
=
plot
plot
=
ggplot
(
df_d
,
aes
(
y
=
entropy_C1
,
x
=
value
,
shape
=
val_H0Ha
,
col
=
val_H0Ha
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"Entropy C1"
,
x
=
"Value"
)
plot
=
plot
+
xlim
(
c
(
0
,
1
))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C2
),
1
)))
plot
=
plot
+
guides
(
col
=
FALSE
)
plot
=
plot
+
scale_color_manual
(
values
=
colors
)
plot
=
plot
+
geom_vline
(
data
=
df_recall_sup09_per_meth
,
aes
(
xintercept
=
threshold
,
col
=
couple
),
size
=
1
,
show.legend
=
NA
,
linetype
=
"dashed"
)
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_entropy_C1
=
plot
plot
=
ggplot
(
subset
(
df_d
,
val_H0Ha
==
"value_Ha"
)
,
aes
(
y
=
entropy_C2
,
x
=
entropy_C1
,
shape
=
val_H0Ha
,
col
=
value
))
plot
=
plot
+
theme_bw
()
plot
=
plot
+
theme
(
legend.position
=
"top"
)
plot
=
plot
+
labs
(
y
=
"Entropy C2"
,
x
=
"Entropy C1"
)
plot
=
plot
+
xlim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C1
),
1
)))
+
ylim
(
c
(
0
,
max
(
max
(
df_d
$
entropy_C2
),
1
)))
plot
=
plot
+
geom_point
(
size
=
1.2
,
alpha
=
0.7
,
stroke
=
0.01
)
plot
=
plot
+
scale_shape_manual
(
values
=
c
(
16
,
17
))
plot
=
plot
+
scale_colour_gradientn
(
colours
=
c
(
"red"
,
"yellow"
,
"green"
,
"lightblue"
,
"darkblue"
),
values
=
c
(
1.0
,
0.8
,
0.6
,
0.4
,
0.2
,
0
))
plot
=
plot
+
facet_grid
(
couple
~
methode
)
plot
=
plot
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
))
plot_entropy_C2_C1
=
plot
save_plot
(
paste0
(
opt
$
out
,
suffix
,
".value_distance_per_meth.pdf"
),
plot_value_JSD
,
ncol
=
0.4
*
length
(
unique
(
df_d
$
methode
)),
nrow
=
0.4
*
length
(
unique
(
df_d
$
couple
)),
base_aspect_ratio
=
1
,
limitsize
=
FALSE
)
save_plot
(
paste0
(
opt
$
out
,
suffix
,
".value_distance_per_meth.pdf"
),
plot_value_JSD
,
ncol
=
0.4
*
length
(
unique
(
df_d
$
methode
)),
nrow
=
0.4
*
length
(
unique
(
df_d
$
couple
)),
base_aspect_ratio
=
1
,
limitsize
=
FALSE
)
#plot = plot_grid(plot_recall_precision,plot_max_MCC,plot_value_JSD,plot_value_ED,plot_entropy_C2_C1,plot_entropy_C1,plot_entropy_C2,
# labels = c("A", "B","C","D","E","F"),
# rel_heights = c(length(unique(df_out$couple))*0.8,3,length(unique(df_out$couple))*0.8,length(unique(df_out$couple))*0.8,length(unique(df_out$couple))*0.8,length(unique(df_out$couple))*0.8,length(unique(df_out$couple))*0.8),
# nrow=7
# )
}
plot
=
plot_grid
(
plot_recall_precision
,
plot_recall_precision_papier
,
plot_max_MCC
,
plot_FPR
,
plot_FPR2
,
labels
=
c
(
"A"
,
"A'"
,
"B"
,
"B'"
,
"B''"
),
rel_heights
=
c
(
length
(
unique
(
df_out
$
couple
))
*
0.8
,
2
,
4
,
2
,
2
),
...
...
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