tengfei/ggbio — Issue #7: TODO in Milestone 2.0
Author: tengfei
Created: 2011-11-01 18:13:40+00:00
State: open

* update qplot for GRangesList, make fill,color work , also main/xlab/ylab, to show splicing summary, make height of rectangle an option.
* what's is default xlim??how to make it flexible?
* we need an option that essentially does a keepSeqlevels(x, unique(seqnames(x))). This is similar to the 'drop' parameter of split(). That one defaults to FALSE, but I think we should default to TRUE.
* either show only the interval with data or show all of the seqlevels in their entirety.The user should also be able to override this logic with their own xlim() setting
* function(..., xlim = default_xlim(x, restrict), restrict = TRUE), 'default_xlim' either picks the data range or the seqlevels, depending on 'restrict'.to show a partial signature of qplot(). And yes default_xlim() would be in ggbio.
* use the extents of the data as the default seqlengths.
* IGB sliced view, now is facet_gr as parameter, make it more GoG, probably, + facet_gr().or implement it as coordinates system
* when y-axis labels doesn't have meanings like levels, hide it
* GenomicRangesList
* geom problem: geom is a CharacterList, then you take each element as the geoms for the corresponding track. Otherwise, you "recycle" the given character vector to apply those geoms to all tracks.
* smarter track: We also have to think about smarter track layout. in this case we have one dataset and can use faceting. What happens when we have multiple datasets on each sample and still want to lay things out by sample? It would seems that our GenomicRangesList of tracks should have elementMetadata with variables that we could "facet" by. put the elementMetadata on the GenomicRangesList, so that each element (track) is guaranteed to have the same number of columns. This is a really important feature. In ggplot2, you only plot a single dataset at a time, but one of the primary goals of genomic visualization is to expose relationships across datasets by drawing them along the genome. So we need multiple datasets. This is an important point for the paper.
* API dicussion(lazy evaluation and S4 issues)
* API should allow the user embed our qplot function inside and how?