Changelog

Source: NEWS.md

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