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Gael MILLOT
cute_little_R_functions
Commits
3f25c8ff
Commit
3f25c8ff
authored
Jan 07, 2021
by
Gael
Browse files
reorganization
parent
1553bf22
Changes
26
Hide whitespace changes
Inline
Side-by-side
check/check_dataset.R
0 → 100644
View file @
3f25c8ff
################ CREATION OF THE CHECKING DATASET
######## object list t25_20201108 (25 objects created 20201108)
vec1
<-
-1
:
3
# vector of integers
vec2
<-
1
:
3
/
3
# vector of proportions
vec3
<-
c
(
1
,
2
,
NA
,
-
Inf
)
# vector of integers but stored as "double", with NA and Inf
vec4
<-
"pearson"
# vector of characters
vec5
<-
c
(
"a"
,
"b"
,
"a"
,
NA
)
# vector of characters with NA
cpx1
<-
as.complex
(
1
)
# complex
mat1
<-
matrix
(
vec1
)
# 1D matrix of integers
mat2
<-
matrix
(
c
(
1
:
5
,
NA
),
ncol
=
2
,
dimnames
=
list
(
c
(
"ROW1"
,
"ROW2"
,
"ROW3"
),
c
(
"M1"
,
"M2"
)))
# 2D matrix of floats with NA
df1
<-
as.data.frame
(
mat2
)
# data.frame
l1
<-
list
(
L1
=
1
:
3
,
L2
=
letters
[
1
:
3
])
# list
fac1
<-
factor
(
rep
(
letters
[
4
:
6
],
c
(
4
:
6
)))
# factor
tab1
<-
table
(
fac1
)
# 1D table
tab2
<-
table
(
fac1
,
fac1
)
# 2D table
exp1
<-
expression
(
"a"
)
# object of class "expression", mode "expression" & type "expression"
name1
<-
substitute
(
exp1
)
# object of class "name", mode "name" & type "symbol"
fun1
<-
mean
# closure function of class "function", mode "function" & type "closure"
fun2
<-
sum
# primitive function of class "function", mode "function" & type "builtin"
fun3
<-
get
(
"<-"
)
# primitive function of class "function", mode "function" & type "special"
env1
<-
new.env
()
# environment
s4.1
<-
show
# S4 object
call1
<-
call
(
"call1"
)
# object of class "call", mode "call" & type "language"
t25_20201108
<-
list
(
# test list
NULL
,
NA
,
1
,
TRUE
,
vec1
,
vec2
,
vec3
,
vec4
,
vec5
,
cpx1
,
mat1
,
mat2
,
df1
,
l1
,
fac1
,
tab1
,
tab2
,
exp1
,
name1
,
fun1
,
fun2
,
fun3
,
env1
,
s4.1
,
call1
)
save
(
list
=
c
(
"vec1"
,
"vec2"
,
"vec3"
,
"vec4"
,
"vec5"
,
"cpx1"
,
"mat1"
,
"mat2"
,
"df1"
,
"l1"
,
"fac1"
,
"tab1"
,
"tab2"
,
"exp1"
,
"name1"
,
"fun1"
,
"fun2"
,
"fun3"
,
"env1"
,
"s4.1"
,
"call1"
,
"t25_20201108"
),
file
=
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/check/check_dataset.t25_20201108.RData"
)
######## object list t26_20201124 (26 objects created 20201124)
vec1
<-
-1
:
3
# vector of integers
vec2
<-
1
:
3
/
3
# vector of proportions
vec3
<-
c
(
1
,
2
,
NA
,
-
Inf
)
# vector of integers but stored as "double", with NA and Inf
vec4
<-
"pearson"
# vector of characters
vec5
<-
c
(
"a"
,
"b"
,
"a"
,
NA
)
# vector of characters with NA
cpx1
<-
as.complex
(
1
)
# complex
mat1
<-
matrix
(
vec1
)
# 1D matrix of integers
mat2
<-
matrix
(
c
(
1
:
5
,
NA
),
ncol
=
2
,
dimnames
=
list
(
c
(
"ROW1"
,
"ROW2"
,
"ROW3"
),
c
(
"M1"
,
"M2"
)))
# 2D matrix of floats with NA
df1
<-
as.data.frame
(
mat2
)
# data.frame
df2
<-
data.frame
(
df1
,
CAT
=
letters
[
1
:
nrow
(
df1
)])
# data.frame
l1
<-
list
(
L1
=
1
:
3
,
L2
=
letters
[
1
:
3
])
# list
fac1
<-
factor
(
rep
(
letters
[
4
:
6
],
c
(
4
:
6
)))
# factor
tab1
<-
table
(
fac1
)
# 1D table
tab2
<-
table
(
fac1
,
fac1
)
# 2D table
exp1
<-
expression
(
"a"
)
# object of class "expression", mode "expression" & type "expression"
name1
<-
substitute
(
exp1
)
# object of class "name", mode "name" & type "symbol"
fun1
<-
mean
# closure function of class "function", mode "function" & type "closure"
fun2
<-
sum
# primitive function of class "function", mode "function" & type "builtin"
fun3
<-
get
(
"<-"
)
# primitive function of class "function", mode "function" & type "special"
env1
<-
new.env
()
# environment
s4.1
<-
show
# S4 object
call1
<-
call
(
"call1"
)
# object of class "call", mode "call" & type "language"
t26_20201124
<-
list
(
# test list
NULL
,
NA
,
1
,
TRUE
,
vec1
,
vec2
,
vec3
,
vec4
,
vec5
,
cpx1
,
mat1
,
mat2
,
df1
,
df2
,
l1
,
fac1
,
tab1
,
tab2
,
exp1
,
name1
,
fun1
,
fun2
,
fun3
,
env1
,
s4.1
,
call1
)
save
(
list
=
c
(
"vec1"
,
"vec2"
,
"vec3"
,
"vec4"
,
"vec5"
,
"cpx1"
,
"mat1"
,
"mat2"
,
"df1"
,
"df2"
,
"l1"
,
"fac1"
,
"tab1"
,
"tab2"
,
"exp1"
,
"name1"
,
"fun1"
,
"fun2"
,
"fun3"
,
"env1"
,
"s4.1"
,
"call1"
,
"t26_20201124"
),
file
=
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/check/check_dataset.t26_20201124.RData"
)
######## object list t8_20201126 (8 objects created 20201126)
cor1
<-
list
(
-1
,
0
,
1
)
# vector of integers
prop1
<-
list
(
0
,
0.5
,
1
)
# vector of proportions
int1
<-
list
(
0
,
2
,
4
)
# vector of positive integers
int2
<-
list
(
0
,
10
,
20
)
# vector of positive integers
angle1
<-
list
(
-90
,
0
,
45
,
90
,
180
)
# vector of positive integers
log1
<-
list
(
"no"
,
"log2"
,
"log10"
)
# vector of characters
logic1
<-
list
(
TRUE
,
FALSE
)
# vector of logic
path1
<-
list
(
"C:\\Program Files\\R\\R-4.0.2\\library\\"
)
t8_20201126
<-
list
(
# test list
cor1
,
prop1
,
int1
,
int2
,
angle1
,
log1
,
logic1
,
path1
)
save
(
list
=
c
(
"cor1"
,
"prop1"
,
"int1"
,
"int2"
,
"angle1"
,
"log1"
,
"logic1"
,
"path1"
,
"t8_20201126"
),
file
=
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/check/check_dataset.t8_20201126.RData"
)
################ END CREATION OF THE CHECKING DATASET
other/test
_dataset.t25_20201108.RData
→
check/check
_dataset.t25_20201108.RData
View file @
3f25c8ff
File moved
other/test
_dataset.t26_20201124.RData
→
check/check
_dataset.t26_20201124.RData
View file @
3f25c8ff
File moved
other/test
_dataset.t8_20201126.RData
→
check/check
_dataset.t8_20201126.RData
View file @
3f25c8ff
File moved
check/check_fun_check.R
0 → 100644
View file @
3f25c8ff
######## fun_check() #### check class, type, length, etc., of objects
# 20201216 checking each argument separately, with default values for the others
load
(
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/other/check_dataset.t26_20201124.RData"
)
# recover the test list tl file
source
(
"https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/7ceacbc07ba1cc65b3dd8db53ef0d8db2a2823d7/cute_little_R_functions.R"
)
# performed with check_dataset.RData commited 20201107 (25 different objects)
# in green the values that are not the default values
path
<-
"C:\\Users\\Gael\\Desktop\\fun_check_test1\\"
for
(
i0
in
1
:
14
){
Sys.sleep
(
1
)
cat
(
"\n\nLOOP "
,
i0
,
" / 14\n\n"
)
res
<-
fun_test
(
fun
=
"fun_check"
,
arg
=
c
(
L1
=
"data"
,
L2
=
"class"
,
L3
=
"typeof"
,
L4
=
"mode"
,
L5
=
"length"
,
L6
=
"prop"
,
L7
=
"double.as.integer.allowed"
,
L8
=
"options"
,
L9
=
"all.options.in.data"
,
L10
=
"na.contain"
,
L11
=
"neg.values"
,
L12
=
"print"
,
L13
=
"data.name"
,
L14
=
"fun.name"
),
val
=
list
(
L1
=
if
(
i0
==
1
){
t26_20201124
}
else
{
"a"
},
L2
=
if
(
i0
==
2
){
t26_20201124
}
else
{
"vector"
},
L3
=
if
(
i0
==
3
){
t26_20201124
}
else
{
list
(
NULL
)},
L4
=
if
(
i0
==
4
){
t26_20201124
}
else
{
list
(
NULL
)},
L5
=
if
(
i0
==
5
){
t26_20201124
}
else
{
list
(
NULL
)},
L6
=
if
(
i0
==
6
){
t26_20201124
}
else
{
FALSE
},
L7
=
if
(
i0
==
7
){
t26_20201124
}
else
{
FALSE
},
L8
=
if
(
i0
==
8
){
t26_20201124
}
else
{
list
(
NULL
)},
L9
=
if
(
i0
==
9
){
t26_20201124
}
else
{
FALSE
},
L10
=
if
(
i0
==
10
){
t26_20201124
}
else
{
FALSE
},
L11
=
if
(
i0
==
11
){
t26_20201124
}
else
{
TRUE
},
L12
=
if
(
i0
==
12
){
t26_20201124
}
else
{
FALSE
},
L13
=
if
(
i0
==
13
){
t26_20201124
}
else
{
"test.function"
},
L14
=
if
(
i0
==
14
){
t26_20201124
}
else
{
list
(
NULL
)}
),
thread.nb
=
NULL
,
plot.fun
=
FALSE
,
export
=
TRUE
,
res.path
=
path
)
}
file.list
<-
list.files
(
path
,
full.names
=
TRUE
)
tempo.df
<-
NULL
for
(
i0
in
1
:
length
(
file.list
)){
tempo.df
<-
rbind
(
tempo.df
,
cbind
(
loop
=
paste0
(
"loop_"
,
i0
),
read.table
(
list.files
(
file.list
[
i0
],
,
full.names
=
TRUE
)[
grepl
(
x
=
list.files
(
file.list
[
i0
]),
pattern
=
"^table_from_fun_test.*"
)],
header
=
TRUE
,
sep
=
"\t"
,
comment.char
=
""
)))
}
write.table
(
tempo.df
,
file
=
paste0
(
path
,
"/final_table_from_fun_test.txt"
),
row.names
=
FALSE
,
col.names
=
TRUE
,
append
=
FALSE
,
quote
=
FALSE
,
sep
=
"\t"
,
eol
=
"\n"
,
na
=
""
)
# 20201216 checking all the possible values of each argument, with default values for the others
load
(
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/other/check_dataset.t26_20201124.RData"
)
# recover the test list tl file
load
(
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/other/check_dataset.t8_20201126.RData"
)
# recover the test list tl file
source
(
"https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/7ceacbc07ba1cc65b3dd8db53ef0d8db2a2823d7/cute_little_R_functions.R"
)
# performed with check_dataset.RData commited 20201107 (25 different objects)
# in green the values that are not the default values
path
<-
"C:\\Users\\Gael\\Desktop\\fun_check_test2\\"
for
(
i0
in
1
:
14
){
Sys.sleep
(
1
)
cat
(
"\n\nLOOP "
,
i0
,
" / 14\n\n"
)
res
<-
fun_test
(
fun
=
"fun_check"
,
arg
=
c
(
L1
=
"data"
,
L2
=
"class"
,
L3
=
"typeof"
,
L4
=
"mode"
,
L5
=
"length"
,
L6
=
"prop"
,
L7
=
"double.as.integer.allowed"
,
L8
=
"options"
,
L9
=
"all.options.in.data"
,
L10
=
"na.contain"
,
L11
=
"neg.values"
,
L12
=
"print"
,
L13
=
"data.name"
,
L14
=
"fun.name"
),
val
=
list
(
L1
=
if
(
i0
==
1
){
t26_20201124
}
else
{
"a"
},
L2
=
if
(
i0
==
2
){
list
(
NULL
,
"vector"
,
"logical"
,
"integer"
,
"numeric"
,
"complex"
,
"character"
,
"matrix"
,
"array"
,
"data.frame"
,
"list"
,
"factor"
,
"table"
,
"expression"
,
"name"
,
"symbol"
,
"function"
,
"uneval"
,
"environment"
,
"ggplot2"
,
"ggplot_built"
,
"call"
)}
else
if
(
i0
==
8
){
list
(
NULL
)}
else
{
"vector"
},
L3
=
if
(
i0
==
3
){
list
(
NULL
,
"logical"
,
"integer"
,
"double"
,
"complex"
,
"character"
,
"list"
,
"expression"
,
"symbol"
,
"closure"
,
"special"
,
"builtin"
,
"environment"
,
"S4"
,
"language"
)}
else
{
list
(
NULL
)},
L4
=
if
(
i0
==
4
){
list
(
NULL
,
"logical"
,
"numeric"
,
"complex"
,
"character"
,
"list"
,
"expression"
,
"name"
,
"symbol"
,
"function"
,
"environment"
,
"S4"
,
"call"
)}
else
{
list
(
NULL
)},
L5
=
if
(
i0
==
5
){
list
(
NULL
,
0
,
2
,
4
)}
else
{
list
(
NULL
)},
L6
=
if
(
i0
==
6
){
logic1
}
else
{
FALSE
},
L7
=
if
(
i0
==
7
){
logic1
}
else
{
FALSE
},
L8
=
if
(
i0
==
8
){
list
(
NULL
,
"a"
)}
else
{
list
(
NULL
)},
L9
=
if
(
i0
==
9
){
logic1
}
else
{
FALSE
},
L10
=
if
(
i0
==
10
){
logic1
}
else
{
FALSE
},
L11
=
if
(
i0
==
11
){
logic1
}
else
{
TRUE
},
L12
=
if
(
i0
==
12
){
logic1
}
else
{
TRUE
},
L13
=
if
(
i0
==
13
){
list
(
NULL
,
"test.function"
)}
else
{
list
(
NULL
)},
L14
=
if
(
i0
==
14
){
list
(
NULL
,
"FUN_NAME"
)}
else
{
list
(
NULL
)}
),
thread.nb
=
NULL
,
plot.fun
=
FALSE
,
export
=
TRUE
,
res.path
=
path
)
}
file.list
<-
list.files
(
path
,
full.names
=
TRUE
)
tempo.df
<-
NULL
for
(
i0
in
1
:
length
(
file.list
)){
tempo.df
<-
rbind
(
tempo.df
,
cbind
(
loop
=
paste0
(
"loop_"
,
i0
),
read.table
(
list.files
(
file.list
[
i0
],
,
full.names
=
TRUE
)[
grepl
(
x
=
list.files
(
file.list
[
i0
]),
pattern
=
"^table_from_fun_test.*"
)],
header
=
TRUE
,
sep
=
"\t"
,
comment.char
=
""
)))
}
write.table
(
tempo.df
,
file
=
paste0
(
path
,
"/final_table_from_fun_test.txt"
),
row.names
=
FALSE
,
col.names
=
TRUE
,
append
=
FALSE
,
quote
=
FALSE
,
sep
=
"\t"
,
eol
=
"\n"
,
na
=
""
)
check/check_fun_gg_boxplot.R
0 → 100644
View file @
3f25c8ff
# 20201126 checking each argument separately, with default values for the others
load
(
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/other/check_dataset.t26_20201124.RData"
)
# recover the test list tl file
source
(
"https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/7ceacbc07ba1cc65b3dd8db53ef0d8db2a2823d7/cute_little_R_functions.R"
)
# performed with check_dataset.RData commited 20201107 (25 different objects)
# in green the values that are not the default values
path
<-
"C:\\Users\\Gael\\Desktop\\fun_boxplot_test1\\"
for
(
i0
in
1
:
57
){
Sys.sleep
(
1
)
cat
(
"\n\nLOOP "
,
i0
,
" / 57\n\n"
)
res
<-
fun_test
(
fun
=
"fun_gg_boxplot"
,
arg
=
c
(
L1
=
"data1"
,
L2
=
"y"
,
L3
=
"categ"
,
L4
=
"categ.class.order"
,
L5
=
"categ.color"
,
L6
=
"box.legend.name"
,
L7
=
"box.fill"
,
L8
=
"box.width"
,
L9
=
"box.space"
,
L10
=
"box.line.size"
,
L11
=
"box.notch"
,
L12
=
"box.alpha"
,
L13
=
"box.mean"
,
L14
=
"box.whisker.kind"
,
L15
=
"box.whisker.width"
,
L16
=
"dot.color"
,
L17
=
"dot.categ"
,
L18
=
"dot.categ.class.order"
,
L19
=
"dot.legend.name"
,
L20
=
"dot.tidy"
,
L21
=
"dot.tidy.bin.nb"
,
L22
=
"dot.jitter"
,
L23
=
"dot.seed"
,
L24
=
"dot.size"
,
L25
=
"dot.alpha"
,
L26
=
"dot.border.size"
,
L27
=
"dot.border.color"
,
L28
=
"x.lab"
,
L29
=
"x.angle"
,
L30
=
"y.lab"
,
L31
=
"y.lim"
,
L32
=
"y.log"
,
L33
=
"y.tick.nb"
,
L34
=
"y.second.tick.nb"
,
L35
=
"y.include.zero"
,
L36
=
"y.top.extra.margin"
,
L37
=
"y.bottom.extra.margin"
,
L38
=
"stat.disp"
,
L39
=
"stat.disp.mean"
,
L40
=
"stat.size"
,
L41
=
"stat.dist"
,
L42
=
"stat.angle"
,
L43
=
"vertical"
,
L44
=
"text.size"
,
L45
=
"title"
,
L46
=
"title.text.size"
,
L47
=
"legend.show"
,
L48
=
"legend.width"
,
L49
=
"article"
,
L50
=
"grid"
,
L51
=
"add"
,
L52
=
"return"
,
L53
=
"return.ggplot"
,
L54
=
"return.gtable"
,
L55
=
"plot"
,
L56
=
"warn.print"
,
L57
=
"lib.path"
),
val
=
list
(
L1
=
if
(
i0
==
1
){
t26_20201124
}
else
{
list
(
df2
)},
L2
=
if
(
i0
==
2
){
t26_20201124
}
else
{
"M1"
},
L3
=
if
(
i0
==
3
){
t26_20201124
}
else
{
"CAT"
},
L4
=
if
(
i0
==
4
){
t26_20201124
}
else
{
list
(
NULL
)},
L5
=
if
(
i0
==
5
){
t26_20201124
}
else
{
list
(
NULL
)},
L6
=
if
(
i0
==
6
){
t26_20201124
}
else
{
list
(
NULL
)},
L7
=
if
(
i0
==
7
){
t26_20201124
}
else
{
FALSE
},
L8
=
if
(
i0
==
8
){
t26_20201124
}
else
{
0.5
},
L9
=
if
(
i0
==
9
){
t26_20201124
}
else
{
0.1
},
L10
=
if
(
i0
==
10
){
t26_20201124
}
else
{
0.75
},
L11
=
if
(
i0
==
11
){
t26_20201124
}
else
{
FALSE
},
L12
=
if
(
i0
==
12
){
t26_20201124
}
else
{
1
},
L13
=
if
(
i0
==
13
){
t26_20201124
}
else
{
TRUE
},
L14
=
if
(
i0
==
14
){
t26_20201124
}
else
{
"std"
},
L15
=
if
(
i0
==
15
){
t26_20201124
}
else
{
0
},
L16
=
if
(
i0
==
16
){
t26_20201124
}
else
{
grey
(
0.25
)},
L17
=
if
(
i0
==
17
){
t26_20201124
}
else
{
list
(
NULL
)},
L18
=
if
(
i0
==
18
){
t26_20201124
}
else
{
list
(
NULL
)},
L19
=
if
(
i0
==
19
){
t26_20201124
}
else
{
list
(
NULL
)},
L20
=
if
(
i0
==
20
){
t26_20201124
}
else
{
FALSE
},
L21
=
if
(
i0
==
21
){
t26_20201124
}
else
{
50
},
L22
=
if
(
i0
==
22
){
t26_20201124
}
else
{
0.5
},
L23
=
if
(
i0
==
23
){
t26_20201124
}
else
{
2
},
L24
=
if
(
i0
==
24
){
t26_20201124
}
else
{
3
},
L25
=
if
(
i0
==
25
){
t26_20201124
}
else
{
0.5
},
L26
=
if
(
i0
==
26
){
t26_20201124
}
else
{
0.5
},
L27
=
if
(
i0
==
27
){
t26_20201124
}
else
{
list
(
NULL
)},
L28
=
if
(
i0
==
28
){
t26_20201124
}
else
{
list
(
NULL
)},
L29
=
if
(
i0
==
29
){
t26_20201124
}
else
{
0
},
L30
=
if
(
i0
==
30
){
t26_20201124
}
else
{
list
(
NULL
)},
L31
=
if
(
i0
==
31
){
t26_20201124
}
else
{
list
(
NULL
)},
L32
=
if
(
i0
==
32
){
t26_20201124
}
else
{
"no"
},
L33
=
if
(
i0
==
33
){
t26_20201124
}
else
{
list
(
NULL
)},
L34
=
if
(
i0
==
34
){
t26_20201124
}
else
{
1
},
L35
=
if
(
i0
==
35
){
t26_20201124
}
else
{
FALSE
},
L36
=
if
(
i0
==
36
){
t26_20201124
}
else
{
0.05
},
L37
=
if
(
i0
==
37
){
t26_20201124
}
else
{
0.05
},
L38
=
if
(
i0
==
38
){
t26_20201124
}
else
{
"top"
},
L39
=
if
(
i0
==
39
){
t26_20201124
}
else
{
FALSE
},
L40
=
if
(
i0
==
40
){
t26_20201124
}
else
{
4
},
L41
=
if
(
i0
==
41
){
t26_20201124
}
else
{
5
},
L42
=
if
(
i0
==
42
){
t26_20201124
}
else
{
0
},
L43
=
if
(
i0
==
43
){
t26_20201124
}
else
{
TRUE
},
L44
=
if
(
i0
==
44
){
t26_20201124
}
else
{
12
},
L45
=
if
(
i0
==
45
){
t26_20201124
}
else
{
""
},
L46
=
if
(
i0
==
46
){
t26_20201124
}
else
{
8
},
L47
=
if
(
i0
==
47
){
t26_20201124
}
else
{
TRUE
},
L48
=
if
(
i0
==
48
){
t26_20201124
}
else
{
0.5
},
L49
=
if
(
i0
==
49
){
t26_20201124
}
else
{
TRUE
},
L50
=
if
(
i0
==
50
){
t26_20201124
}
else
{
FALSE
},
L51
=
if
(
i0
==
51
){
t26_20201124
}
else
{
list
(
NULL
)},
L52
=
if
(
i0
==
52
){
t26_20201124
}
else
{
FALSE
},
L53
=
if
(
i0
==
53
){
t26_20201124
}
else
{
FALSE
},
L54
=
if
(
i0
==
54
){
t26_20201124
}
else
{
TRUE
},
L55
=
if
(
i0
==
55
){
t26_20201124
}
else
{
TRUE
},
L56
=
if
(
i0
==
56
){
t26_20201124
}
else
{
TRUE
},
L57
=
if
(
i0
==
57
){
t26_20201124
}
else
{
list
(
NULL
)}
),
thread.nb
=
NULL
,
plot.fun
=
FALSE
,
export
=
TRUE
,
res.path
=
path
)
}
file.list
<-
list.files
(
path
,
full.names
=
TRUE
)
tempo.df
<-
NULL
for
(
i0
in
1
:
length
(
file.list
)){
tempo.df
<-
rbind
(
tempo.df
,
cbind
(
loop
=
paste0
(
"loop_"
,
i0
),
read.table
(
list.files
(
file.list
[
i0
],
full.names
=
TRUE
)[
grepl
(
x
=
list.files
(
file.list
[
i0
]),
pattern
=
"^table_from_fun_test.*"
)],
header
=
TRUE
,
sep
=
"\t"
,
comment.char
=
""
)))
}
write.table
(
tempo.df
,
file
=
paste0
(
path
,
"/final_table_from_fun_test.txt"
),
row.names
=
FALSE
,
col.names
=
TRUE
,
append
=
FALSE
,
quote
=
FALSE
,
sep
=
"\t"
,
eol
=
"\n"
,
na
=
""
)
# 20201126 checking all the possible values of each argument, with default values for the others
load
(
"C:/Users/gael/Documents/Git_projects/cute_little_R_functions/other/check_dataset.t8_20201126.RData"
)
# recover the test list tl file
source
(
"https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/7ceacbc07ba1cc65b3dd8db53ef0d8db2a2823d7/cute_little_R_functions.R"
)
# performed with check_dataset.RData commited 20201107 (25 different objects)
# in green the values that are not the default values
path
<-
"C:\\Users\\Gael\\Desktop\\fun_boxplot_test2\\"
### Data set
set.seed
(
1
)
obs1
<-
data.frame
(
Time
=
c
(
rnorm
(
20
,
100
,
10
),
rnorm
(
20
,
200
,
50
),
rnorm
(
20
,
500
,
60
),
rep
(
NA
,
20
)),
Categ1
=
rep
(
c
(
"CAT"
,
"DOG"
),
times
=
40
),
Categ2
=
rep
(
c
(
"A"
,
"B"
,
"C"
,
"D"
),
each
=
20
),
Color1
=
rep
(
c
(
"coral"
,
"lightblue"
),
times
=
40
),
Color2
=
rep
(
c
(
"#9F2108"
,
"#306100"
,
"#007479"
,
"#8500C0"
),
each
=
20
),
stringsAsFactors
=
TRUE
)
set.seed
(
NULL
)
### end Data set
for
(
i0
in
1
:
57
){
Sys.sleep
(
1
)
cat
(
"\n\nLOOP "
,
i0
,
" / 57\n\n"
)
res
<-
fun_test
(
fun
=
"fun_gg_boxplot"
,
arg
=
c
(
L1
=
"data1"
,
L2
=
"y"
,
L3
=
"categ"
,
L4
=
"categ.class.order"
,
L5
=
"categ.color"
,
L6
=
"box.legend.name"
,
L7
=
"box.fill"
,
L8
=
"box.width"
,
L9
=
"box.space"
,
L10
=
"box.line.size"
,
L11
=
"box.notch"
,
L12
=
"box.alpha"
,
L13
=
"box.mean"
,
L14
=
"box.whisker.kind"
,
L15
=
"box.whisker.width"
,
L16
=
"dot.color"
,
L17
=
"dot.categ"
,
L18
=
"dot.categ.class.order"
,
L19
=
"dot.legend.name"
,
L20
=
"dot.tidy"
,
L21
=
"dot.tidy.bin.nb"
,
L22
=
"dot.jitter"
,
L23
=
"dot.seed"
,
L24
=
"dot.size"
,
L25
=
"dot.alpha"
,
L26
=
"dot.border.size"
,
L27
=
"dot.border.color"
,
L28
=
"x.lab"
,
L29
=
"x.angle"
,
L30
=
"y.lab"
,
L31
=
"y.lim"
,
L32
=
"y.log"
,
L33
=
"y.tick.nb"
,
L34
=
"y.second.tick.nb"
,
L35
=
"y.include.zero"
,
L36
=
"y.top.extra.margin"
,
L37
=
"y.bottom.extra.margin"
,
L38
=
"stat.disp"
,
L39
=
"stat.disp.mean"
,
L40
=
"stat.size"
,
L41
=
"stat.dist"
,
L42
=
"stat.angle"
,
L43
=
"vertical"
,
L44
=
"text.size"
,
L45
=
"title"
,
L46
=
"title.text.size"
,
L47
=
"legend.show"
,
L48
=
"legend.width"
,
L49
=
"article"
,
L50
=
"grid"
,
L51
=
"add"
,
L52
=
"return"
,
L53
=
"return.ggplot"
,
L54
=
"return.gtable"
,
L55
=
"plot"
,
L56
=
"warn.print"
,
L57
=
"lib.path"
),
val
=
list
(