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biopet.biopet
Commits
b5ea73df
Commit
b5ea73df
authored
Mar 21, 2017
by
Peter van 't Hof
Browse files
Remove duplicated scripts
parent
ae0dbeaf
Changes
3
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
deleted
100644 → 0
View file @
ae0dbeaf
library
(
reshape2
)
library
(
ggplot2
)
library
(
argparse
)
parser
<-
ArgumentParser
(
description
=
'Process some integers'
)
parser
$
add_argument
(
'--input'
,
dest
=
'input'
,
type
=
'character'
,
help
=
'Input tsv file'
,
required
=
TRUE
)
parser
$
add_argument
(
'--output'
,
dest
=
'output'
,
type
=
'character'
,
help
=
'Output png file'
,
required
=
TRUE
)
parser
$
add_argument
(
'--width'
,
dest
=
'width'
,
type
=
'integer'
,
default
=
500
)
parser
$
add_argument
(
'--height'
,
dest
=
'height'
,
type
=
'integer'
,
default
=
500
)
parser
$
add_argument
(
'--xlabel'
,
dest
=
'xlabel'
,
type
=
'character'
)
parser
$
add_argument
(
'--ylabel'
,
dest
=
'ylabel'
,
type
=
'character'
,
required
=
TRUE
)
parser
$
add_argument
(
'--llabel'
,
dest
=
'llabel'
,
type
=
'character'
)
parser
$
add_argument
(
'--title'
,
dest
=
'title'
,
type
=
'character'
)
parser
$
add_argument
(
'--removeZero'
,
dest
=
'removeZero'
,
type
=
'character'
,
default
=
"false"
)
arguments
<-
parser
$
parse_args
()
png
(
filename
=
arguments
$
output
,
width
=
arguments
$
width
,
height
=
arguments
$
height
)
DF
<-
read.table
(
arguments
$
input
,
header
=
TRUE
)
if
(
is.null
(
arguments
$
xlabel
))
xlab
<-
colnames
(
DF
)[
1
]
else
xlab
<-
arguments
$
xlabel
colnames
(
DF
)[
1
]
<-
"Rank"
DF1
<-
melt
(
DF
,
id.var
=
"Rank"
)
if
(
arguments
$
removeZero
==
"true"
)
DF1
<-
DF1
[
DF1
$
value
>
0
,
]
if
(
arguments
$
removeZero
==
"true"
)
print
(
"Removed 0 values"
)
ggplot
(
DF1
,
aes
(
x
=
Rank
,
y
=
value
,
group
=
variable
,
color
=
variable
))
+
xlab
(
xlab
)
+
ylab
(
arguments
$
ylabel
)
+
guides
(
fill
=
guide_legend
(
title
=
arguments
$
llabel
))
+
theme
(
axis.text.x
=
element_text
(
angle
=
90
,
hjust
=
1
,
size
=
8
))
+
ggtitle
(
arguments
$
title
)
+
theme_bw
()
+
geom_point
()
dev.off
()
biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
deleted
100644 → 0
View file @
ae0dbeaf
library
(
reshape2
)
library
(
ggplot2
)
library
(
argparse
)
parser
<-
ArgumentParser
(
description
=
'Process some integers'
)
parser
$
add_argument
(
'--input'
,
dest
=
'input'
,
type
=
'character'
,
help
=
'Input tsv file'
,
required
=
TRUE
)
parser
$
add_argument
(
'--output'
,
dest
=
'output'
,
type
=
'character'
,
help
=
'Output png file'
,
required
=
TRUE
)
parser
$
add_argument
(
'--width'
,
dest
=
'width'
,
type
=
'integer'
,
default
=
500
)
parser
$
add_argument
(
'--height'
,
dest
=
'height'
,
type
=
'integer'
,
default
=
500
)
parser
$
add_argument
(
'--xlabel'
,
dest
=
'xlabel'
,
type
=
'character'
)
parser
$
add_argument
(
'--ylabel'
,
dest
=
'ylabel'
,
type
=
'character'
,
required
=
TRUE
)
parser
$
add_argument
(
'--llabel'
,
dest
=
'llabel'
,
type
=
'character'
)
parser
$
add_argument
(
'--title'
,
dest
=
'title'
,
type
=
'character'
)
parser
$
add_argument
(
'--removeZero'
,
dest
=
'removeZero'
,
type
=
'character'
,
default
=
"false"
)
arguments
<-
parser
$
parse_args
()
png
(
filename
=
arguments
$
output
,
width
=
arguments
$
width
,
height
=
arguments
$
height
)
DF
<-
read.table
(
arguments
$
input
,
header
=
TRUE
)
if
(
is.null
(
arguments
$
xlabel
))
xlab
<-
colnames
(
DF
)[
1
]
else
xlab
<-
arguments
$
xlabel
colnames
(
DF
)[
1
]
<-
"Rank"
DF1
<-
melt
(
DF
,
id.var
=
"Rank"
)
if
(
arguments
$
removeZero
==
"true"
)
DF1
<-
DF1
[
DF1
$
value
>
0
,
]
if
(
arguments
$
removeZero
==
"true"
)
print
(
"Removed 0 values"
)
ggplot
(
DF1
,
aes
(
x
=
Rank
,
y
=
value
,
group
=
variable
,
color
=
variable
))
+
xlab
(
xlab
)
+
ylab
(
arguments
$
ylabel
)
+
guides
(
fill
=
guide_legend
(
title
=
arguments
$
llabel
))
+
theme
(
axis.text.x
=
element_text
(
angle
=
90
,
hjust
=
1
,
size
=
8
))
+
ggtitle
(
arguments
$
title
)
+
theme_bw
()
+
geom_line
()
dev.off
()
biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
deleted
100644 → 0
View file @
ae0dbeaf
library
(
reshape2
)
library
(
ggplot2
)
library
(
argparse
)
parser
<-
ArgumentParser
(
description
=
'Process some integers'
)
parser
$
add_argument
(
'--input'
,
dest
=
'input'
,
type
=
'character'
,
help
=
'Input tsv file'
,
required
=
TRUE
)
parser
$
add_argument
(
'--output'
,
dest
=
'output'
,
type
=
'character'
,
help
=
'Output png file'
,
required
=
TRUE
)
parser
$
add_argument
(
'--width'
,
dest
=
'width'
,
type
=
'integer'
,
default
=
500
)
parser
$
add_argument
(
'--height'
,
dest
=
'height'
,
type
=
'integer'
,
default
=
500
)
parser
$
add_argument
(
'--xlabel'
,
dest
=
'xlabel'
,
type
=
'character'
)
parser
$
add_argument
(
'--ylabel'
,
dest
=
'ylabel'
,
type
=
'character'
,
required
=
TRUE
)
parser
$
add_argument
(
'--llabel'
,
dest
=
'llabel'
,
type
=
'character'
)
parser
$
add_argument
(
'--title'
,
dest
=
'title'
,
type
=
'character'
)
arguments
<-
parser
$
parse_args
()
png
(
filename
=
arguments
$
output
,
width
=
arguments
$
width
,
height
=
arguments
$
height
)
DF
<-
read.table
(
arguments
$
input
,
header
=
TRUE
)
if
(
is.null
(
arguments
$
xlabel
))
xlab
<-
colnames
(
DF
)[
1
]
else
xlab
<-
arguments
$
xlabel
colnames
(
DF
)[
1
]
<-
"Rank"
DF1
<-
melt
(
DF
,
id.var
=
"Rank"
)
ggplot
(
DF1
,
aes
(
x
=
Rank
,
y
=
value
,
fill
=
variable
))
+
xlab
(
xlab
)
+
ylab
(
arguments
$
ylabel
)
+
guides
(
fill
=
guide_legend
(
title
=
arguments
$
llabel
))
+
theme
(
axis.text.x
=
element_text
(
angle
=
90
,
hjust
=
1
,
size
=
8
))
+
geom_bar
(
stat
=
"identity"
,
width
=
1
)
+
ggtitle
(
arguments
$
title
)
dev.off
()
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