# derfinderPlot 1.21.4 SIGNIFICANT USER-VISIBLE CHANGES * Documentation website is now available at http://leekgroup.github.io/derfinderPlot/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown. # derfinderPlot 1.21.3 SIGNIFICANT USER-VISIBLE CHANGES * Code in all examples has been re-styled thanks to styler::style_pkg(), see dev/02_update.R for details. # derfinderPlot 1.21.2 SIGNIFICANT USER-VISIBLE CHANGES * Switched from Travis to GitHub actions through usethis. * Build the documentation website automatically with pkgdown. * Added a dev/01_setup.R script. * Now using a README.Rmd file. # derfinderPlot 1.21.1 SIGNIFICANT USER-VISIBLE CHANGES * Use GenomeInfoDb::getChromInfoFromUCSC() when possible instead of data from biovizBase::hg19Ideogram for getting the hg19 chromosome lengths. # derfinderPlot 1.19.3 SIGNIFICANT USER-VISIBLE CHANGES * Added a `NEWS.md` file to track changes to the package. # derfinderPlot 1.17.2 NEW FEATURES * Add ORCID's following changes at http://bioconductor.org/developers/package-guidelines/#description # derfinderPlot 1.15.1 SIGNIFICANT USER-VISIBLE CHANGES * Use BiocManager # derfinderPlot 1.13.5 BUG FIXES * Fixed an issue in `plotCluster()` on how it was loading the `hg19IdeogramCyto` object from the `biovizBase` package. # derfinderPlot 1.13.4 BUG FIXES * Fixed an issue with a call to `GenomicRanges::gaps()` that affected how the introns were plotting in `plotRegionCoverage()` when the underlying data has a specifying start and end of the chromosome (that is, a `seqinfo()` with `seqlengths` specified). Thanks to Emily E Burke for reporting this issue https://github.com/emilyburke. # derfinderPlot 1.11.2 SIGNIFICANT USER-VISIBLE CHANGES * Vignette now uses the new `BiocStyle::html_document()` that was recently released. # derfinderPlot 1.7.10 SIGNIFICANT USER-VISIBLE CHANGES * Help pages now document advanced arguments. # derfinderPlot 1.7.8 BUG FIXES * Updated links to BrainSpan. Issue reported by Steve Semick https://github.com/SteveSemick. # derfinderPlot 1.7.1 SIGNIFICANT USER-VISIBLE CHANGES * Dropped defunct functions. # derfinderPlot 1.5.8 BUG FIXES * `plotRegionCoverage()` used to take into account the strand of the regions for finding transcripts that overlapped the regions. This was not a problem with DERs from derfinder since they have strand `*` by default but it is a problem when using it with stranded regions. * `plotCluster()` will also now ignore strand for finding neighboring regions. # derfinderPlot 1.5.4 SIGNIFICANT USER-VISIBLE CHANGES * Only use distance if it's not `NA` in `plotRegionCoverage()` # derfinderPlot 1.3.4 SIGNIFICANT USER-VISIBLE CHANGES * Dropped `tMatrix()` because it was a confusing plot and also lead to build errors. # derfinderPlot 1.3.3 NEW FEATURES * Added the function `tMatrix()` which uses a `GRanges` object that has a variable of interest to compute t-Statistics between bins of the genome. For each bin, the values of the variable of interest from the regions overlapping the bin are used. We use t-Statistics instead of correlation because not all bins will have the same number of regions. This type of plot is similar to interaction plots made for HiC data. # derfinderPlot 1.3.2 NEW FEATURES * Added the `vennRegions()` function to visualize how many regions overlap known exons, introns, intergenic regions, none of them or several of these groups. # derfinderPlot 1.3.1 SIGNIFICANT USER-VISIBLE CHANGES * Deprecated functions with underscores in their names in favor of camelCase functions. This was done to simplify the package. # derfinderPlot 1.1.6 SIGNIFICANT USER-VISIBLE CHANGES * Adapted to work with `bumphunter` version >= 1.7.6 # derfinderPlot 1.1.3 BUG FIXES * Adapted `plotCluster()` and `plotOverview()` to derfinder 1.1.5 # derfinderPlot 0.99.0 NEW FEATURES * Preparing to submit to Bioconductor. * Added tests and vignette. SIGNIFICANT USER-VISIBLE CHANGES * `plotOverview()` and `plotCluster()` can now plot FWER adjusted p-values if calculated with `derfinder::mergeResults()` # derfinderPlot 0.0.4 SIGNIFICANT USER-VISIBLE CHANGES * Hid some arguments in `plotCluster()` and `plotOverview()` as advanced just like in `derfinder` v0.0.74 BUG FIXES * Improved the speed in `plotRegionCoverage()` then `txdb` is specified. Also fixed the introns on the gene track. # derfinderPlot 0.0.3 SIGNIFICANT USER-VISIBLE CHANGES * `plotRegionCoverage()` now has a `txdb` argument. When specified, this function will extract the transcript information needed and display the transcripts. # derfinderPlot 0.0.1 SIGNIFICANT USER-VISIBLE CHANGES * Moved plotting functions from derfinder into this package