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hem
hamlet
Commits
9de43e5e
Commit
9de43e5e
authored
Jun 25, 2020
by
van den Berg
Browse files
Merge branch 'devel' into 'master'
Use the tools library to determine file extension See merge request
!8
parents
4a0dc089
449e555b
Pipeline
#4269
failed with stages
in 41 minutes and 55 seconds
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1
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3
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includes/snv-indels/scripts/plotVariants.R
View file @
9de43e5e
...
...
@@ -5,6 +5,7 @@
# Copyright (c) 2015 Leiden University Medical Center <http://lumc.nl>
# All rights reserved.
library
(
"tools"
)
suppressMessages
(
library
(
Gviz
))
RenameEnsemblChroms
<-
function
(
annots
)
{
...
...
@@ -359,7 +360,7 @@ MakePlot <- function(parsed.data, sample.name, gene.id, gene.model, genome = "hg
plot.title
<-
paste
(
c
(
"Variant Calls - Sample '"
,
sample.name
,
"'\n"
,
gene.symbol
,
" ("
,
gene.id
,
")"
),
collapse
=
""
)
if
(
!
is.null
(
out.file
)
&
tolower
(
unlist
(
strsplit
(
out.file
,
"\\."
))[
-1
]
)
==
"png"
)
{
if
(
!
is.null
(
out.file
)
&
file_ext
(
out.file
)
==
"png"
)
{
png
(
out.file
,
height
=
to.plot
$
height
,
width
=
to.plot
$
width
)
Gviz
::
plotTracks
(
to.plot
$
tracks
,
chromosome
=
chrom
,
main
=
plot.title
,
col
=
NULL
,
sizes
=
to.plot
$
sizes
)
...
...
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