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biopet.biopet
Commits
fc98fc55
Commit
fc98fc55
authored
Jun 08, 2015
by
Peter van 't Hof
Browse files
Auto scale plots on number of samples/libraries
parent
f2645096
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
fc98fc55
...
...
@@ -83,7 +83,9 @@ object BammetricsReport extends ReportBuilder {
plot
.
input
=
tsvFile
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Reads"
)
plot
.
width
=
Some
(
1200
)
if
(
libraryLevel
)
{
plot
.
width
=
Some
(
200
+
(
summary
.
libraries
.
filter
(
s
=>
sampleId
.
getOrElse
(
s
.
_1
)
==
s
.
_1
).
foldLeft
(
0
)(
_
+
_
.
_2
.
size
)
*
10
))
}
else
plot
.
width
=
Some
(
200
+
(
summary
.
samples
.
filter
(
s
=>
sampleId
.
getOrElse
(
s
)
==
s
).
size
*
10
))
plot
.
title
=
Some
(
"Aligned reads"
)
plot
.
runLocal
()
}
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
fc98fc55
...
...
@@ -87,7 +87,7 @@ object FlexiprepReport extends ReportBuilder {
plot
.
input
=
tsvFile
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Reads"
)
plot
.
width
=
Some
(
750
)
plot
.
width
=
Some
(
200
+
(
summary
.
libraries
.
filter
(
s
=>
sampleId
.
getOrElse
(
s
.
_1
)
==
s
.
_1
).
foldLeft
(
0
)(
_
+
_
.
_2
.
size
)
*
10
)
)
plot
.
title
=
Some
(
"QC summary on "
+
read
+
" reads"
)
plot
.
runLocal
()
}
...
...
@@ -128,7 +128,7 @@ object FlexiprepReport extends ReportBuilder {
plot
.
input
=
tsvFile
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"Bases"
)
plot
.
width
=
Some
(
750
)
plot
.
width
=
Some
(
200
+
(
summary
.
libraries
.
filter
(
s
=>
sampleId
.
getOrElse
(
s
.
_1
)
==
s
.
_1
).
foldLeft
(
0
)(
_
+
_
.
_2
.
size
)
*
10
)
)
plot
.
title
=
Some
(
"QC summary on "
+
read
+
" bases"
)
plot
.
runLocal
()
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
fc98fc55
...
...
@@ -129,7 +129,9 @@ object ShivaReport extends MultisampleReportBuilder {
plot
.
input
=
tsvFile
plot
.
output
=
pngFile
plot
.
ylabel
=
Some
(
"VCF records"
)
plot
.
width
=
Some
(
1200
)
if
(
libraryLevel
)
{
plot
.
width
=
Some
(
200
+
(
summary
.
libraries
.
filter
(
s
=>
sampleId
.
getOrElse
(
s
.
_1
)
==
s
.
_1
).
foldLeft
(
0
)(
_
+
_
.
_2
.
size
)
*
10
))
}
else
plot
.
width
=
Some
(
200
+
(
summary
.
samples
.
filter
(
s
=>
sampleId
.
getOrElse
(
s
)
==
s
).
size
*
10
))
plot
.
runLocal
()
}
}
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