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GenomeGraphs
Added Rd files for makeTranscript, makeGene and makeGeneRegion

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GenomeGraphs
Added Rd files for makeTranscript, makeGene and makeGeneRegion
Some additions and slight changes to vignette, also addition of makeAnnotationTrack function.
Added makeGene, makeTranscript and makeGeneRegion, still need to add man pages for these and do some extra checking
Added overlay to ExonArray example

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GenomeGraphs
Added overlay to ExonArray example
Added a plot to the vignette from the paper.
Added most make functions and initial man pages, replaced dummyData by exampleData
A couple of small additions

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GenomeGraphs
Forgot to add the Overlay.R file :)

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GenomeGraphs
Forgot to add the Overlay.R file :)
According to a number of patches from Elizabeth Purdom (many thanks!) The following changes have been made:
*.) drawOverlay : changed added to Overlay.R -- modified code to be TextOverlay, RectangleOverlay. Additional refactoring should occur where we remove arguments/member-variables from TextOverlay which are irrelevant. Added helper functions of the form:
to <- makeTextOverlay(text = "Some Text!", xpos = .5, ypos = .5, coords = "absolute")
*.) Added the TextOverlay class.
*.) Added fill, and color arguments to the RectangleOverlay to support the coloring of the rectangle lines and the innards separately.
*.) Added showDisplayOptions, which either takes an object, or a character string and prints out the DisplayPars that the object expects.
*.) Added method drawGD for Segmentation class
*.) .drawSegments now can do vectorized coloring and different lwd for elements of the Segmentation list.
*.) Added convenience function segmentation to construct segmentation objects more readily -- this tries to make that clunky list format less of a pain.
*.) Made a number of tweaks for better displaying the legend. Added convenience function for making legends
*.) fixed a display bug in Transcript
*.) added labelRot, labelColor, and labelCex for the gdPlot function.

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GenomeGraphs
Modified some help pages fixed the R CHECK problem.

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GenomeGraphs
Some minore changes that probably break things.

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GenomeGraphs
Added plotId functionality to the AnnotationTrack object

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GenomeGraphs
Added plotId functionality to the AnnotationTrack object

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GenomeGraphs
Some reasonably large changes which will probably mess up R CMD CHECK, but need to get these in here at some point. They include a new object which should replace the various forms of annotation plotting.

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GenomeGraphs
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

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GenomeGraphs
Fixed a typo in biocViews (Microarrays -> Microarray).

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GenomeGraphs
Commiting a small number of changes: made the drawGD method public, allowed for the biomart member variable of a GeneRegion to be NULL - this change is to allow for the introduction of a annotationSource object.

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GenomeGraphs
Added a HighlightRegion class which allows the vertical delineation of regions of interest through tracks.

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GenomeGraphs
Slight change for clearer documentation on arguments of gdPlot
Bumped version number to 0.99.1 so the package can be included in the upcoming Bioc release
This adds package GenomeGraphs to bioconductor.

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