v1.2.0

Additions

• Functionality around defining "clusters"/"Idents" has been revamped but backwards compatible. Added argument alt_ident in many functions including vizAPOTC and RunAPOTC to allow for counting clusters based on different cell identities or the current active identity if NULL, and it is now part of the subsetting arguments for all functions that work with APackOfTheClones runs /data. This includes:
  • vizAPOTC
  • RunAPOTC
  • getSharedClones
  • countCloneSizes (see section below in changes to incorporate identity functionality)
  • updated relevant vignettes to reflect the new argument.
• Add renameApotcRun to rename APackOfTheClones runs.
• Add argument detail in APOTCPlot and vizAPOTC to allow user to quickly plot a version of the clonal expansion plot where each cluster is just one large circle. Correspondingly added a subsection in vignette("APackOfTheClones-shared").
• Add argument publicity in getSharedClones to filter the output shared clones by the number of clusters each clonotype is present in.

Changes

• vizAPOTC and RunAPOTC now defaults to aggregating clustered clonotype frequencies based on active ident of the seurat object. Additionally, if using an ident where its levels are not ordered integers, then the cluster labels for each APackOfTheClones run that is stored in the seurat object will no longer just be "C1", "C2", ... and will be the names of the idents.
• Fixed the output for arguments intop and intop_per_cl in getSharedClones so they actually filters for all clones with clone sizes in the top range.
• All arguments in AdjustAPOTC that asks for cluster indices as input now also accept characters representing their respective labels in the APackOfTheClones runs.
• The argument recolor_indicies has been renamed to recolor_indices in AdjustAPOTC.
• countCloneSizes now outputs a named list with each name being the cluster identity. Additionally, the argument by_cluster can now also take in single characters as arguments representing possible alternative cluster identities in the metadata.
• Removed mini_seurat_obj from publicly exported data.
• Several exported functions, including AdjustAPOTC, now have stricter argument checking of type and length.
• Package can now be installed again on releases with C++14 compilation on older releases of R.
• The minimum required R version has been bumped from 4.0.0 to 4.1.0.