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 Modifier,GRanges
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for Modifier
plotData(
x,
name,
from,
to,
type = NA,
showSequenceData = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for Modifier
getDataTrack(x, name = name, ...)
# S4 method for ModifierSet,GRanges
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for ModifierSet
plotData(
x,
name,
from,
to,
type = NA,
showSequenceData = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for SequenceData,GRanges
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for SequenceData
plotData(
x,
name,
from,
to,
perTranscript = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for SequenceData
getDataTrack(x, name = name, ...)
# S4 method for SequenceDataList
getDataTrack(x, name = name, ...)
# S4 method for SequenceDataList,GRanges
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for SequenceDataList
plotData(
x,
name,
from,
to,
perTranscript = FALSE,
showSequence = TRUE,
showAnnotation = FALSE,
...
)
# S4 method for SequenceDataSet
getDataTrack(x, name = name, ...)
# S4 method for SequenceDataSet,GRanges
plotDataByCoord(x, coord, type = NA, window.size = 15L, ...)
# S4 method for 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) {
plotData(msi, "2", from = 10L, to = 45L)
}