R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 25 found.
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AlignedReadTrack-class (Package: Gviz) : AlignedReadTrack class and methods (NOTE: THIS IS STILL IN

A class to represent short sequences that have been aligned to a reference genome as they are typically generated in a next generation sequencing experiment.

● Data Source: BioConductor
● Keywords: classes
● Alias: AlignedReadTrack, AlignedReadTrack-class, [,AlignedReadTrack,ANY,ANY-method, [,AlignedReadTrack-method, coverage,AlignedReadTrack-method, drawAxis,AlignedReadTrack-method, drawGD,AlignedReadTrack-method, drawGrid,AlignedReadTrack-method, initialize,AlignedReadTrack-method, setCoverage,AlignedReadTrack-method, show,AlignedReadTrack-method, split,AlignedReadTrack,ANY-method, split,AlignedReadTrack-method, subset,AlignedReadTrack-method
● 2 images

AlignmentsTrack-class (Package: Gviz) : AlignmentsTrack class and methods

A class to represent short sequences that have been aligned to a reference genome as they are typically generated in next generation sequencing experiments.

● Data Source: BioConductor
● Keywords: classes
● Alias: AlignmentsTrack, AlignmentsTrack-class, chromosome<-,AlignmentsTrack-method, drawAxis,AlignmentsTrack-method, drawGD,AlignmentsTrack-method
● 5 images

AnnotationTrack-class (Package: Gviz) : AnnotationTrack class and methods

A fairly generic track object for arbitrary genomic range annotations, with the option of grouped track items. The extended DetailsAnnotationTrack provides a more flexible interface to add user-defined custom information for each range.

● Data Source: BioConductor
● Keywords: classes
● Alias: AnnotationTrack, AnnotationTrack-class, DetailsAnnotationTrack, DetailsAnnotationTrack-class, coerce,AnnotationTrack,UCSCData-method, coerce,GRanges,AnnotationTrack-method, coerce,GRangesList,AnnotationTrack-method, collapseTrack,AnnotationTrack-method, consolidateTrack,AnnotationTrack-method, drawGD,AnnotationTrack-method, drawGrid,AnnotationTrack-method, group, group,AnnotationTrack-method, group<-, group<-,AnnotationTrack,character-method, identifier, identifier,AnnotationTrack-method, identifier<-, identifier<-,AnnotationTrack,character-method, initialize,AnnotationTrack-method, initialize,DetailsAnnotationTrack-method, initialize,ReferenceAnnotationTrack-method, setStacks,AnnotationTrack-method, show,AnnotationTrack-method, show,ReferenceAnnotationTrack-method, subset,AnnotationTrack-method, subset,ReferenceAnnotationTrack-method
● 7 images

BiomartGeneRegionTrack-class (Package: Gviz) : BiomartGeneRegionTrack class and methods

A class to hold gene model data for a genomic region fetched dynamically from EBI's Biomart Ensembl data source.

● Data Source: BioConductor
● Keywords: classes
● Alias: BiomartGeneRegionTrack, BiomartGeneRegionTrack-class, initialize,BiomartGeneRegionTrack-method, subset,BiomartGeneRegionTrack-method
● 6 images

CustomTrack-class (Package: Gviz) : CustomTrack class and methods

A fully customizable track object to be populated via a user-defined plotting function.

● Data Source: BioConductor
● Keywords: classes
● Alias: CustomTrack, CustomTrack-class, drawGD,CustomTrack-method, initialize,CustomTrack-method, show,CustomTrack-method
● 0 images

DataTrack-class (Package: Gviz) : DataTrack class and methods

A class to store numeric data values along genomic coordinates. Multiple samples as well as sample groupings are supported, with the restriction of equal genomic coordinates for a single observation across samples.

● Data Source: BioConductor
● Keywords: classes
● Alias: DataTrack, DataTrack-class, [,DataTrack,ANY,ANY-method, [,DataTrack-method, coerce,DataTrack,data.frame-method, coerce,GRanges,DataTrack-method, collapseTrack,DataTrack-method, drawAxis,DataTrack-method, drawGD,DataTrack-method, feature,DataTrack-method, feature<-,DataTrack,character-method, initialize,DataTrack-method, initialize,ReferenceDataTrack-method, range,DataTrack-method, score,DataTrack-method, show,DataTrack-method, show,ReferenceDataTrack-method, split,DataTrack,ANY-method, split,DataTrack-method, strand,DataTrack-method, strand<-,DataTrack,ANY-method, strand<-,DataTrack-method, subset,DataTrack-method, subset,ReferenceDataTrack-method, values,DataTrack-method, values<-,DataTrack-method
● 2 images

DisplayPars-class (Package: Gviz) : DisplayPars class and method

All tracks within this package are highly customizable. The DisplayPars class facilitates this and provides a unified API to the customization parameters.

● Data Source: BioConductor
● Keywords: classes
● Alias: DisplayPars, DisplayPars-class, as.list,DisplayPars-method, as.list,InferredDisplayPars-method, availableDisplayPars, coerce,DisplayPars,list-method, coerce,InferredDisplayPars,list-method, displayPars,DisplayPars,character-method, displayPars,DisplayPars,missing-method, displayPars<-, displayPars<-,DisplayPars,list-method, getPar, getPar,DisplayPars,character-method, getPar,DisplayPars,missing-method, head,InferredDisplayPars-method, initialize,DisplayPars-method, setPar, setPar,DisplayPars,character-method, setPar,DisplayPars,list-method, show,DisplayPars-method, tail,InferredDisplayPars-method
● 0 images

GdObject-class (Package: Gviz) : GdObject class and methods

The virtual parent class for all track items in the Gviz package. This class definition contains all the common entities that are needed for a track to be plotted. During object instantiation for any of the sub-classes inheriting from GdObject, this class' global ininitializer has to be called in order to assure that all necessary settings are present.

● Data Source: BioConductor
● Keywords: classes
● Alias: GdObject, GdObject-class, chromosome,GdObject-method, chromosome<-,GdObject-method, consolidateTrack, consolidateTrack,GdObject-method, coords, coords,GdObject-method, coords,NULL-method, displayPars,GdObject,character-method, displayPars,GdObject,missing-method, displayPars<-,GdObject,list-method, drawAxis,GdObject-method, drawGD, drawGD,DetailsAnnotationTrack-method, drawGD,GeneRegionTrack-method, drawGD,SequenceTrack-method, drawGrid,GdObject-method, genome<-,GdObject-method, getPar,GdObject,character-method, getPar,GdObject,missing-method, group,GdObject-method, imageMap, imageMap,GdObject-method, initialize,GdObject-method, isActiveSeq<-,GdObject-method, names,GdObject-method, names<-,GdObject,character-method, setPar,GdObject,character-method, setPar,GdObject,list-method, subset,GdObject-method, tags, tags,GdObject-method, tags,NULL-method
● 0 images

GeneRegionTrack-class (Package: Gviz) : GeneRegionTrack class and methods

A class to hold gene model data for a genomic region.

● Data Source: BioConductor
● Keywords: classes
● Alias: GeneRegionTrack, GeneRegionTrack-class, coerce,GRanges,GeneRegionTrack-method, coerce,GRangesList,GeneRegionTrack-method, coerce,GeneRegionTrack,UCSCData-method, coerce,TxDb,GeneRegionTrack-method, collapseTrack,GeneRegionTrack-method, exon, exon,GeneRegionTrack-method, exon<-, exon<-,GeneRegionTrack,character-method, gene, gene,GeneRegionTrack-method, gene<-, gene<-,GeneRegionTrack,character-method, group,GeneRegionTrack-method, group<-,GeneRegionTrack,character-method, identifier,GeneRegionTrack-method, identifier<-,GeneRegionTrack,character-method, initialize,GeneRegionTrack-method, initialize,ReferenceGeneRegionTrack-method, show,GeneRegionTrack-method, show,ReferenceGeneRegionTrack-method, subset,ReferenceGeneRegionTrack-method, symbol, symbol,GeneRegionTrack-method, symbol<-, symbol<-,GeneRegionTrack,character-method, transcript, transcript,GeneRegionTrack-method, transcript<-, transcript<-,GeneRegionTrack,character-method
● 7 images

GenomeAxisTrack-class (Package: Gviz) : GenomeAxisTrack class and methods

A class representing a customizable genomic axis.

● Data Source: BioConductor
● Keywords: classes
● Alias: GenomeAxisTrack, GenomeAxisTrack-class, [,GenomeAxisTrack,ANY,ANY-method, [,GenomeAxisTrack-method, collapseTrack,GenomeAxisTrack-method, drawGD,GenomeAxisTrack-method, end,GenomeAxisTrack-method, end<-,GenomeAxisTrack-method, initialize,GenomeAxisTrack-method, length,GenomeAxisTrack-method, range,GenomeAxisTrack-method, ranges,GenomeAxisTrack-method, ranges<-,GenomeAxisTrack-method, show,GenomeAxisTrack-method, start,GenomeAxisTrack-method, start<-,GenomeAxisTrack-method, strand,GenomeAxisTrack-method, subset,GenomeAxisTrack-method, values,GenomeAxisTrack-method, width,GenomeAxisTrack-method
● 6 images