Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Open sidebar
VEBER Philippe
codepi
Commits
d5954698
Commit
d5954698
authored
Sep 06, 2018
by
Carine Rey
Committed by
LANORE Vincent
Sep 12, 2018
Browse files
update tdg09 FDR -> LRT + plot
parent
b0512326
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
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 @
d5954698
...
...
@@ -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 @
d5954698
...
...
@@ -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 @
d5954698
...
...
@@ -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 @
d5954698
...
...
@@ -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"
]]
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment