plotData {RNAmodR} | R Documentation |
SequenceData
,
SequenceDataSet
, SequenceDataList
, Modifier
or
ModifierSet
object.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 signature 'Modifier,GRanges' plotDataByCoord(x, coord, type = NA, window.size = 15L, ...) ## S4 method for signature 'Modifier' plotData( x, name, from, to, type = NA, showSequenceData = FALSE, showSequence = TRUE, showAnnotation = FALSE, ... ) ## S4 method for signature 'Modifier' getDataTrack(x, name = name, ...) ## S4 method for signature 'ModifierSet,GRanges' plotDataByCoord(x, coord, type = NA, window.size = 15L, ...) ## S4 method for signature 'ModifierSet' plotData( x, name, from, to, type = NA, showSequenceData = FALSE, showSequence = TRUE, showAnnotation = FALSE, ... ) ## S4 method for signature 'SequenceData,GRanges' plotDataByCoord(x, coord, type = NA, window.size = 15L, ...) ## S4 method for signature 'SequenceData' plotData( x, name, from, to, perTranscript = FALSE, showSequence = TRUE, showAnnotation = FALSE, ... ) ## S4 method for signature 'SequenceData' getDataTrack(x, name = name, ...) ## S4 method for signature 'SequenceDataList' getDataTrack(x, name = name, ...) ## S4 method for signature 'SequenceDataList,GRanges' plotDataByCoord(x, coord, type = NA, window.size = 15L, ...) ## S4 method for signature 'SequenceDataList' plotData( x, name, from, to, perTranscript = FALSE, showSequence = TRUE, showAnnotation = FALSE, ... ) ## S4 method for signature 'SequenceDataSet' getDataTrack(x, name = name, ...) ## S4 method for signature 'SequenceDataSet,GRanges' plotDataByCoord(x, coord, type = NA, window.size = 15L, ...) ## S4 method for signature 'SequenceDataSet' plotData( x, name, from, to, perTranscript = FALSE, showSequence = TRUE, showAnnotation = FALSE, ... )
x |
a |
name |
Only for |
from |
Only for |
to |
Only for |
type |
the data type of data show as data tracks. |
... |
optional parameters:
|
coord |
coordinates of a positions to subset to as a
|
window.size |
integer value for the number of positions on the left and
right site of the selected positions included in the plotting (default:
|
showSequenceData |
|
showSequence |
|
showAnnotation |
|
perTranscript |
|
a plot send to the active graphic device
data(msi,package="RNAmodR") plotData(msi[[1]], "2", from = 10L, to = 45L) ## Not run: plotData(msi, "2", from = 10L, to = 45L) ## End(Not run)