| DisplayPars |
DisplayPars constructs objects of type DisplayPars which are used to effect the display of gdObjects |
| DisplayPars-class |
Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| drawGD |
Generic called on each gdObject to do the plotting. |
| drawGD,AnnotationTrack-method |
Class "AnnotationTrack" |
| drawGD,BaseTrack-method |
Class "BaseTrack" represents base specific data |
| drawGD,ExonArray-method |
Class "ExonArray" representing probe level exon array data from Affymetrix |
| drawGD,Gene-method |
Class "Gene" represents the Ensembl Gene level annotation |
| drawGD,GeneModel-method |
Class "GeneModel", represents a custom gene model |
| drawGD,GeneRegion-method |
Class "GeneRegion", representing gene structures in a defined genomic region |
| drawGD,GenericArray-method |
Class "GenericArray", representing array data |
| drawGD,GenomeAxis-method |
Class "GenomeAxis", representing a genomic coordinate axis |
| drawGD,Ideogram-method |
Class "Ideogram", represent an Ideogram |
| drawGD,Legend-method |
Class "Legend", represents a legend to add to a plot |
| drawGD,MappedRead-method |
Represents mapped reads |
| drawGD,Segmentation-method |
Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| drawGD,Title-method |
Class "Title" representing the title of a plot |
| drawGD,Transcript-method |
Represent known transcript isoforms as annoted by Ensembl |
| drawOverlay, TextOverlay-method |
Class "TextOverlay" |
| drawOverlay,RectangleOverlay-method |
Class "RectangleOverlay" |
| gdObject-class |
Class "gdObject" is the parent class of all of the objects in the system. |
| gdPlot |
gdPlot is the main plotting function of the GenomeGraphs package |
| Gene-class |
Class "Gene" represents the Ensembl Gene level annotation |
| geneBiomart |
AnnotationTrack objects from biomaRt |
| GeneModel-class |
Class "GeneModel", represents a custom gene model |
| GeneRegion-class |
Class "GeneRegion", representing gene structures in a defined genomic region |
| geneRegionBiomart |
Construct an AnnotationTrack object from biomaRt. |
| GenericArray-class |
Class "GenericArray", representing array data |
| GenomeAxis-class |
Class "GenomeAxis", representing a genomic coordinate axis |
| getCex,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| getColor,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| getLty,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| getLwd,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| getPar |
Retrieves a display parameter from an object. |
| getPar,DisplayPars-method |
Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| getPar,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| getPch,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| getPlotId,AnnotationTrack-method |
Class "AnnotationTrack" |
| getPointSize,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| getSegmentation,Segmentable-method |
Class "Segmentable" |
| getSegmentEnd,Segmentation-method |
Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| getSegments,Segmentation-method |
Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| getSegmentStart,Segmentation-method |
Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| getSize,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| segEnd |
Contains dummy copy number segmentation end positions |
| Segmentable-class |
Class "Segmentable" |
| Segmentation-class |
Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| segments |
Contains dummy copy number segment data |
| segStart |
Contains dummy copy number segmentation start positions data |
| seqDataEx |
This is an example data set from chromosome 4 of yeast from various publicly available datasets. |
| setPar |
Sets a display parameter |
| setPar,DisplayPars-method |
Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| setPar,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| show,BaseTrack-method |
Class "BaseTrack" represents base specific data |
| show,DisplayPars-method |
Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| show,ExonArray-method |
Class "ExonArray" representing probe level exon array data from Affymetrix |
| show,Gene-method |
Class "Gene" represents the Ensembl Gene level annotation |
| show,GeneRegion-method |
Class "GeneRegion", representing gene structures in a defined genomic region |
| show,GenericArray-method |
Class "GenericArray", representing array data |
| show,MappedRead-method |
Represents mapped reads |
| show,Transcript-method |
Represent known transcript isoforms as annoted by Ensembl |
| show,TranscriptRegion-method |
Class "TranscriptRegion", representing a genomic region with transcripts |
| showDisplayOptions |
Print standard display options, DisplayPars for an object or a class |
| showDisplayOptions,character-method |
Class "gdObject" is the parent class of all of the objects in the system. |
| showDisplayOptions,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |