GenomeGraphs: Plotting genomic information from Ensembl
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.
- Steffen Durinck <firstname.lastname@example.org>, James Bullard <email@example.com>
- Date of publication
- Steffen Durinck <firstname.lastname@example.org>
- Class "AnnotationTrack"
- Class "BaseTrack" represents base specific data
- Contains dummy copy number data
- DisplayPars constructs objects of type DisplayPars which are...
- Class "DisplayPars" is used to specify graphical parameters...
- Generic called on each gdObject to do the plotting.
- This method does the drawing of a track overlay. One should...
- Class "ExonArray" representing probe level exon array data...
- Contains dummy exon probe positions
- Class "gdObject" is the parent class of all of the objects in...
- gdPlot is the main plotting function of the GenomeGraphs...
- AnnotationTrack objects from biomaRt
- Class "Gene" represents the Ensembl Gene level annotation
- Class "GeneModel", represents a custom gene model
- Construct an AnnotationTrack object from biomaRt.
- Class "GeneRegion", representing gene structures in a defined...
- Class "GenericArray", representing array data
- Class "GenomeAxis", representing a genomic coordinate axis
- Retrieves the genomic range of an object
- Retrieves a display parameter from an object.
- gets the size
- Class "HighlightRegion" is used to highlight vertical blocks...
- Class "Ideogram", represent an Ideogram
- Contains info to plot ideograms
- Class "ImplementsTrackOverlay"
- Contains dummy intensity data
- Class "Legend", represents a legend to add to a plot
- Create objects of class AnnotationTrack
- Creates an object of class BaseTrack
- Creates and object of class ExonArray
- Creates an object of class Gene
- Creates an object of class GeneModel
- Creates an object of class Gene containing the intron-exon...
- Creates an object of class GenericArray
- Creates an object of class GenomeAxis
- Creates object of class Ideogram
- Creates an object of class Legend
- Create a rectangular overlay
- Create objects of class segmentation
- Create objects of class Smoothing
- Create objects of class TextOverlay
- Creates an object of class Title
- Creates an object of class Transcript
- Represents mapped reads
- Class "Overlay"
- Contains dummy expression array probe start positions
- Class "RectangleOverlay"
- Contains dummy copy number segmentation end positions
- Class "Segmentation" is used to specify segmentations to any...
- Contains dummy copy number segment data
- Contains dummy copy number segmentation start positions data
- This is an example data set from chromosome 4 of yeast from...
- Sets a display parameter
- Print standard display options, DisplayPars for an object or...
- Class "Smoothing"
- Class "TextOverlay"
- Class "Title" representing the title of a plot
- Class "TrackOverlay"
- Represent known transcript isoforms as annoted by Ensembl
- Class "TranscriptRegion", representing a genomic region with...
- Contains exon array data
- Contains exon array data
- Contains probe start and end positions of exon array probes
- Contains dummy yeast conservation data
Files in this package