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VEBER Philippe
codepi
Commits
6145bbaf
Commit
6145bbaf
authored
Sep 06, 2018
by
Carine Rey
Browse files
update tdg09 FDR -> LRT + plot
parent
89eb09e8
Changes
4
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4 changed files
with
46 additions
and
17 deletions
+46
-17
lib/convergence_detection.ml
lib/convergence_detection.ml
+2
-2
lib/post_analyses.ml
lib/post_analyses.ml
+4
-1
lib/scripts/calc_t_per_meth.R
lib/scripts/calc_t_per_meth.R
+33
-13
lib/scripts/parse_results_tdg09.py
lib/scripts/parse_results_tdg09.py
+7
-1
No files found.
lib/convergence_detection.ml
View file @
6145bbaf
...
...
@@ -99,7 +99,7 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
|
`Identical_WAG
_
->
"Identical_WAG01"
|
`Topological_LG
_
->
"Topological_LG08"
|
`Topological_WAG
_
->
"Topological_WAG01"
|
`Tdg09
_
->
"Tdg09_1MinusFDR,Tdg09_prob_post"
|
`Tdg09
_
->
"Tdg09_1MinusFDR,Tdg09_
1MinusLRT,Tdg09_
prob_post"
|
`Multinomial
_
->
"Mutinomial_1MinusLRT"
|
`Msd
_
->
"Msd_0.05_1MinusP"
in
...
...
@@ -116,7 +116,7 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
|
`Identical_WAG
_
->
"Identical_WAG01:0.9"
|
`Topological_LG
_
->
"Topological_LG08:0.9"
|
`Topological_WAG
_
->
"Topological_WAG01:0.9"
|
`Tdg09
_
->
"Tdg09_1MinusFDR:0.99,Tdg09_prob_post:0.99"
|
`Tdg09
_
->
"Tdg09_1MinusFDR:0.99,Tdg09_prob_post:0.99
,Tdg09_1MinusLRT:0.99
"
|
`Multinomial
_
->
"Mutinomial_1MinusLRT:0.95"
|
`Msd
_
->
"Msd_0.05_1MinusP:0.95"
...
...
lib/post_analyses.ml
View file @
6145bbaf
...
...
@@ -16,6 +16,7 @@ type t_choices = {
t_choices_recall09
:
text_file
workflow
;
t_choices_plot
:
text_file
workflow
;
t_choices_condensed_plot
:
text_file
workflow
;
t_choices_condensed_plot_png
:
text_file
workflow
;
rp_plot
:
text_file
workflow
;
tree_prefix
:
string
;
}
...
...
@@ -288,9 +289,10 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let
t_choices_complete
=
t_choices_dir
/
selector
[
"out.complete.tsv"
]
in
let
t_choices_plot
=
t_choices_dir
/
selector
[
"out.pdf"
]
in
let
t_choices_condensed_plot
=
t_choices_dir
/
selector
[
"out_condensed.pdf"
]
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
tree_prefix
=
ha_PCOC
.
tree_prefix
in
Some
{
t_choices_max
;
t_choices_recall09
;
t_choices_complete
;
t_choices_plot
;
t_choices_condensed_plot
;
rp_plot
;
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
;
tree_prefix
}
|
_
->
None
...
...
@@ -441,6 +443,7 @@ let repo_of_post_analyses_res ~prefix ~post_analyses_res =
Repo
.[
item
[
prefix
^
".t_choices.pdf"
]
w
.
t_choices_plot
;
item
[
prefix
^
".t_choices.condensed.pdf"
]
w
.
t_choices_condensed_plot
;
item
[
prefix
^
".t_choices.condensed.png"
]
w
.
t_choices_condensed_plot_png
;
item
[
prefix
^
".recall_precision_ok.pdf"
]
w
.
rp_plot
;
]
]
|>
List
.
concat
...
...
lib/scripts/calc_t_per_meth.R
View file @
6145bbaf
...
...
@@ -587,6 +587,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
limitsize
=
FALSE
)
plot_value_JSD
=
NULL
if
(
all
(
c
(
"P_JSD"
,
"P_ED"
,
"C1"
,
"C2"
,
"entropy_C1"
,
"entropy_C2"
)
%in%
colnames
(
df_d
))){
print
(
"plot value/distance"
)
...
...
@@ -673,23 +674,42 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
}
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$couple))*0.8,2,4,2,2),
# nrow=5
#plot = plot_grid(plot_recall_precision,plot_max_MCC,plot_value_JSD,plot_value_ED,plot_entropy_C2_C1,plot_entropy_C1,plot_entropy_C2,
# labels = c("A", "B","C","D","E","F"),
# rel_heights = c(length(unique(df_out$couple))*0.8,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$couple))*0.8,length(unique(df_out$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
),
nrow
=
5
)
if
(
is.null
(
plot_value_JSD
))
{
plot_png
=
plot_grid
(
plot_recall_precision
,
plot_max_MCC
,
labels
=
c
(
"A"
,
"B"
),
rel_heights
=
c
(
1
,
1
),
nrow
=
2
)
}
else
{
plot_png
=
plot_grid
(
plot_recall_precision
,
plot_max_MCC
,
plot_value_JSD
,
labels
=
c
(
"A"
,
"B"
,
"C"
),
rel_heights
=
c
(
0.5
,
0.5
,
1
),
nrow
=
3
)
}
save_plot
(
paste0
(
opt
$
out
,
suffix
,
".pdf"
),
plot
,
ncol
=
0.4
*
length
(
unique
(
df_out_melt
$
methode
)),
nrow
=
length
(
unique
(
df_out
$
couple
))
*
0.5
+
1
+
1
+1
+1
,
nrow
=
length
(
unique
(
df_out
$
couple
))
*
0.5
+
2
+
1
+1
+1
,
base_aspect_ratio
=
1
,
limitsize
=
FALSE
)
save_plot
(
paste0
(
opt
$
out
,
suffix
,
".png"
),
plot_png
,
ncol
=
0.4
*
length
(
unique
(
df_out_melt
$
methode
)),
nrow
=
length
(
unique
(
df_out
$
couple
))
*
1.5
,
base_aspect_ratio
=
1
,
limitsize
=
FALSE
)
...
...
@@ -698,7 +718,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi
plot_out
(
df_out
,
df_d
,
df_recall_sup09_per_meth
,
suffix
=
""
)
condensed_meths
=
c
(
"PCOC"
,
"Diffsel_mean"
,
"Identical_LG08"
,
"Mutinomial_1MinusLRT"
,
"Tdg09_1Minus
FDR
"
,
"Msd_1MinusP"
,
"Msd_0.0
1_1MinusP"
,
"Msd_0.05_1MinusP"
,
"Msd_0.10_1MinusP"
,
"Msd_0.50_1MinusP"
,
"Msd_1.00
_1MinusP"
,
"Topological_LG08"
)
condensed_meths
=
c
(
"PCOC"
,
"Diffsel_mean"
,
"Identical_LG08"
,
"Mutinomial_1MinusLRT"
,
"Tdg09_1Minus
LRT
"
,
"Msd_1MinusP"
,
"Msd_0.0
5
_1MinusP"
,
"Topological_LG08"
)
plot_out
(
df_out
,
df_d
,
df_recall_sup09_per_meth
,
meths
=
condensed_meths
,
suffix
=
"_condensed"
)
...
...
lib/scripts/parse_results_tdg09.py
View file @
6145bbaf
...
...
@@ -43,6 +43,7 @@ Tdg09File.close()
n_sites
=
int
(
searchlines
[
9
].
split
()[
1
])
fdr
=
[
"NA"
]
*
(
n_sites
)
lrt
=
[
"NA"
]
*
(
n_sites
)
prob_post
=
[
"NA"
]
*
(
n_sites
)
for
i
,
line
in
enumerate
(
searchlines
):
...
...
@@ -69,14 +70,18 @@ for i,line in enumerate(searchlines):
lnLconv
=
lnLconv
.
strip
()
lnLnoconv
=
lnLnoconv
.
strip
()
FDR
=
FDR
.
strip
()
LRT
=
LRT
.
strip
()
if
Site
and
FDR
!=
"NA"
:
FDR
=
float
(
FDR
)
LRT
=
float
(
LRT
)
if
FDR
>
1
:
FDR
=
1
fdr
[
int
(
Site
)
-
1
]
=
1
-
FDR
lrt
[
int
(
Site
)
-
1
]
=
1
-
LRT
if
Site
and
FDR
==
"NA"
:
FDR
=
1
fdr
[
int
(
Site
)
-
1
]
=
1
-
FDR
lrt
[
int
(
Site
)
-
1
]
=
0
if
Site
and
lnLconv
!=
"NA"
and
lnLnoconv
!=
"NA"
:
lnLconv
=
float
(
lnLconv
)
...
...
@@ -90,11 +95,12 @@ for i,line in enumerate(searchlines):
Sites
=
[
i
+
1
for
i
in
range
(
n_sites
)]
df_final
=
pd
.
DataFrame
({
'Sites'
:
Sites
,
'Tdg09_1MinusLRT'
:
lrt
,
'Tdg09_1MinusFDR'
:
fdr
,
'Tdg09_prob_post'
:
prob_post
})
df_final
=
df_final
[[
"Sites"
,
"Tdg09_1MinusFDR"
,
"Tdg09_prob_post"
]]
df_final
=
df_final
[[
"Sites"
,
"Tdg09_1MinusFDR"
,
"Tdg09_
1MinusLRT"
,
"Tdg09_
prob_post"
]]
...
...
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