Visualizing data data from a 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 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,
  ...
)

Arguments

x

a SequenceData, SequenceDataSet, SequenceDataList, Modifier or ModifierSet object.

name

Only for plotData: the transcript name

from

Only for plotData: start position

to

Only for plotData: end position

type

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.

coord

coordinates of a positions to subset to as a GRanges object. The 'Parent' column is expected to match the transcript name.

window.size

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)

showSequenceData

TRUE or FALSE: should the sequence data be shown? (default: seqdata = FALSE)

showSequence

TRUE or FALSE: should a sequence track be shown? (default: seqdata = TRUE)

showAnnotation

TRUE or FALSE: should a annotation track be shown? (default: seqdata = FALSE)

perTranscript

TRUE or FALSE: Should the positions shown per transcript? (default: perTranscript = FALSE)

Value

a plot send to the active graphic device

Examples

data(msi,package="RNAmodR")
plotData(msi[[1]], "2", from = 10L, to = 45L)

if (FALSE) { # \dontrun{
plotData(msi, "2", from = 10L, to = 45L)
} # }