v1.0.0

Additions

• Add vizAPOTC to replace clonal_expansion_plot with some similar arguments but works completely differently with an additional set of argument requirements, to ultimately produce a similar but better visualization.
• Add RunAPOTC to store multiple APackOfTheClones runs on the seurat object.
• Add containsApotcRun to check for the existence of some run based on an ID.
• Add getApotcDataIds to get all APackOfTheClones run IDs.
• Add getLastApotcDataId to get the latest APackOfTheClones run ID.
• Add deleteApotcData to delete all data associate with some APackOfTheClones run.
• Add APOTCPlot to plot APackOfTheClones run results into a ggplot.
• Add AdjustAPOTC to modify certain attributes of prior APackOfTheClones runs.
• Add countCloneSizes as a convenience function to count clonotype sizes based on the clonecall and allows subsetting of the seurat metadata
• Add getReductionCentroids as a convenience function to get the physical centroids of each cell in some reduction in a seurat object.
• Added two new vignettes are on the pkgdown website and indexed, and should be viewed in order of vignette("APackOfTheClones") and vignette("APackOfTheClones-runs").

Changes

• ALL v0.1.x functions are deprecated/defunct, and the clonal expansion workflow has changed.
• The latest version two of scRepertoire is now a "dependency", and the package is now structured as an extension of scRepertoire when it comes to integrating VDJ data, as scRepertoire already possesses a mature and common method to do so.
• Package startup message has been modified to notify users about the deprecation and breaking changes.
• All clonal expansion plots will no longer have a title for the default theme