plotData: Visualizing data data from a 'SequenceData',...

In RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

Description

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.

Usage

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,
  ...
)

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)
## Not run: 
plotData(msi, "2", from = 10L, to = 45L)

## End(Not run)

RNAmodR documentation built on Dec. 15, 2020, 2 a.m.