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VEBER Philippe
codepi
Commits
3d8e32a1
Commit
3d8e32a1
authored
Feb 26, 2021
by
Louis Duchemin
Browse files
RERconverge : using Rconsole module to extract results + syntax error fix
parent
c39f81c7
Changes
2
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2 changed files
with
20 additions
and
4 deletions
+20
-4
app/wip.ml
app/wip.ml
+17
-0
lib/R/rer_converge.R
lib/R/rer_converge.R
+3
-4
No files found.
app/wip.ml
View file @
3d8e32a1
...
...
@@ -13,7 +13,24 @@ let marines =
let
pipeline
~
phenotypes
=
Codepi
.
Orthomam
.
rer_converge
~
db
~
phenotypes
()
module
Top
=
Bistro_utils
.
Toplevel_eval
.
Make
(
struct
let
np
=
10
let
mem
=
8
end
)()
let
result_table_script
targets
=
let
open
Codepi
.
R_console
in
let
assignments
=
List
.
map
(
fun
(
clade
,
target
)
->
path
(
Codepi
.
Rer_converge
.
string_of_clade
clade
)
Codepi
.
Orthomam
.(
target
.
result_table
)
)
targets
in
rconsole
(
module
Top
)
"library(tidyverse)"
assignments
let
()
=
result_table_script
(
pipeline
~
phenotypes
:
subterraneans
)
let
main
()
=
try
let
loggers
=
[
Bistro_utils
.
Console_logger
.
create
()
]
in
let
allowed_containers
=
[
`Docker
]
in
...
...
lib/R/rer_converge.R
View file @
3d8e32a1
...
...
@@ -31,8 +31,7 @@ build_traits_paths <-
function
(
phenotypes
,
gene_trees
,
is_continuous
,
useSpecies
=
NULL
,
clade
=
c
(
"ancestral"
,
"terminal"
,
"all"
))
clade
)
{
if
(
is_continuous
)
{
char2Paths
(
phenotypes
,
gene_trees
)
...
...
@@ -40,7 +39,6 @@ build_traits_paths <-
foreground2Tree
(
phenotypes
,
gene_trees
,
clade
=
clade
,
# useSpecies = useSpecies,
plot
=
F
# FIXME : plot=T raises cryptic error
)
%>%
tree2Paths
(
gene_trees
)
...
...
@@ -54,7 +52,8 @@ results = lapply(clades, FUN=function(clade){
traits_paths
<-
build_traits_paths
(
phenotypes
,
gene_trees
,
is_continuous
is_continuous
,
clade
)
res
<-
if
(
is_continuous
)
{
...
...
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