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biopet.biopet
Commits
ebd76709
Commit
ebd76709
authored
Jun 02, 2015
by
Peter van 't Hof
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Add title to some plots
parent
b48a1b0d
Changes
4
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4 changed files
with
9 additions
and
2 deletions
+9
-2
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+1
-0
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
...urces/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
+3
-1
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
.../lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
+3
-1
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+2
-0
No files found.
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
ebd76709
...
...
@@ -84,6 +84,7 @@ object BammetricsReport extends ReportBuilder {
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Reads"
)
plot
.
width
=
Some
(
750
)
plot
.
title
=
Some
(
"Aligned reads"
)
plot
.
runLocal
()
}
...
...
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
View file @
ebd76709
...
...
@@ -10,6 +10,7 @@ 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
()
...
...
@@ -28,6 +29,7 @@ ggplot(DF1, aes(x = Rank, y = value, fill = variable)) +
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
)
geom_bar
(
stat
=
"identity"
,
width
=
1
)
+
ggtitle
(
arguments
$
title
)
dev.off
()
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
View file @
ebd76709
...
...
@@ -23,6 +23,7 @@ class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction
var
xlabel
:
Option
[
String
]
=
config
(
"xlabel"
)
var
ylabel
:
Option
[
String
]
=
config
(
"ylabel"
)
var
llabel
:
Option
[
String
]
=
config
(
"llabel"
)
var
title
:
Option
[
String
]
=
config
(
"title"
)
override
def
cmdLine
:
String
=
super
.
cmdLine
+
required
(
"--input"
,
input
)
+
...
...
@@ -31,5 +32,6 @@ class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction
optional
(
"--height"
,
height
)
+
optional
(
"--xlabel"
,
xlabel
)
+
required
(
"--ylabel"
,
ylabel
)
+
optional
(
"--llabel"
,
llabel
)
optional
(
"--llabel"
,
llabel
)
+
optional
(
"--title"
,
title
)
}
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
ebd76709
...
...
@@ -88,6 +88,7 @@ object FlexiprepReport extends ReportBuilder {
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Reads"
)
plot
.
width
=
Some
(
750
)
plot
.
title
=
Some
(
"QC summary on "
+
read
+
" reads"
)
plot
.
runLocal
()
}
...
...
@@ -128,6 +129,7 @@ object FlexiprepReport extends ReportBuilder {
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Bases"
)
plot
.
width
=
Some
(
750
)
plot
.
title
=
Some
(
"QC summary on "
+
read
+
" bases"
)
plot
.
runLocal
()
}
}
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