SequenceData
, SequenceDataSet
, SequenceDataList
, Modifier
or ModifierSet
object.R/AllGenerics.R
, R/Modifier-viz.R
, R/ModifierSet-viz.R
, and 3 more
plotData.Rd
With the plotData
and plotDataByCoord
functions data
from a SequenceData
, SequenceDataSet
, SequenceDataList
,
Modifier
or ModifierSet
object can be visualized.
Internally the functionality of the Gviz
package is used. For each
SequenceData
and Modifier
class the getDataTrack
is
implemented returning a DataTrack
object
from the Gviz
package.
Positions to be visualized are selected by defining a genomic coordinate,
for which x
has to contain data.
plotData(x, name, from = 1L, to = 30L, type, ...)
plotDataByCoord(x, coord, type, window.size = 15L, ...)
getDataTrack(x, name, ...)
# S4 method for class 'Modifier,GRanges'
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for class 'Modifier'
plotData(
x,
name,
from,
to,
type = NA,
showSequenceData = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for class 'Modifier'
getDataTrack(x, name = name, ...)
# S4 method for class 'ModifierSet,GRanges'
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for class 'ModifierSet'
plotData(
x,
name,
from,
to,
type = NA,
showSequenceData = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for class 'SequenceData,GRanges'
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for class 'SequenceData'
plotData(
x,
name,
from,
to,
perTranscript = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for class 'SequenceData'
getDataTrack(x, name = name, ...)
# S4 method for class 'SequenceDataList'
getDataTrack(x, name = name, ...)
# S4 method for class 'SequenceDataList,GRanges'
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for class 'SequenceDataList'
plotData(
x,
name,
from,
to,
perTranscript = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for class 'SequenceDataSet'
getDataTrack(x, name = name, ...)
# S4 method for class 'SequenceDataSet,GRanges'
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for class 'SequenceDataSet'
plotData(
x,
name,
from,
to,
perTranscript = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
a SequenceData
, SequenceDataSet
,
SequenceDataList
, Modifier
or ModifierSet
object.
Only for plotData
: the transcript name
Only for plotData
: start position
Only for plotData
: end position
the data type of data show as data tracks.
optional parameters:
modified.seq
: TRUE
or FALSE
. Should the sequence
shown with modified nucleotide positions? (default:
modified.seq = FALSE
)
additional.mod
: other modifications, which should be shown
in the annotation and sequence track. The must be a GRanges
compatible
with combineIntoModstrings
.
annotation.track.pars
: Parameters passed onto the
AnnotationTrack
.
sequence.track.pars
: Parameters passed onto the
SequenceTrack
.
coordinates of a positions to subset to as a
GRanges
object. The 'Parent' column is expected to match the
transcript name.
integer value for the number of positions on the left and
right site of the selected positions included in the plotting (default:
window.size = 15L
)
TRUE
or FALSE
: should the sequence data
be shown? (default: seqdata = FALSE
)
TRUE
or FALSE
: should a sequence track be
shown? (default: seqdata = TRUE
)
TRUE
or FALSE
: should a annotation track
be shown? (default: seqdata = FALSE
)
TRUE
or FALSE
: Should the positions shown
per transcript? (default: perTranscript = FALSE
)
a plot send to the active graphic device
data(msi,package="RNAmodR")
plotData(msi[[1]], "2", from = 10L, to = 45L)
if (FALSE) { # \dontrun{
plotData(msi, "2", from = 10L, to = 45L)
} # }