v1.1.0

Additions

• Add getSharedClones to compute information about clonotypes that are present in multiple seurat clusters and return it to the user.
• Add showCloneHighlight to extend the scRepertoire analogue for an APackOfTheClones plot - comes with many options to have certain clones appear differently on an existing plot.
• Add overlayLegend to overlay/modify current legend on a clonal expansion plot.
• Add removeLegend to remove any existing legend on a clonal expansion plot.
• Add mergeCloneSizes to merge clustered raw clone sizes into one table.
• Added arguments in countCloneSizes to optionally NOT get clones sizes by cluster, and to optionally sort the output.
• Added argument add_legend_centerspace in APOTCPlot and vizAPOTC to adjust spacing between guide circles and their values, for cases where guide circles have an exceedingly large radius.
• Added arguments in AdjustAPOTC to work with labels and their locations
• Added argument verbose in APOTCPlot to display some additional visual cues.
• Added argument alpha in APOTCPlot and vizAPOTC to change the alpha (transparency) of each circle.
• Added arguments in APOTCPlot and the corresponding vizAPOTC to compute and plot "links" between clonotypes that are "shared" i.e. common within multiple clusters. Currently, only supports plotting of straight lines.
• Add vignette("APackOfTheClones-install") for detailed installation instructions.
• Add vignette("APackOfTheClones-utils") for more guidance on the various utilities of the package.
• Add vignette("APackOfTheClones-shared") for guidance on working with and visualizing clonotypes shared among different seurat clusters.

Changes

• countCloneSizes
  • Fixed the output to truly be a list of unnamed "table" objects, whereas before, for the clusters with valid clones, each element was instead a list with the first and only element being the tabled clone sizes, and they also had a dimname of "x".
  • Fixed a bug where if the seurat object had no actual clones, the function would error instead of returning a list of empty tables.
  • These fixed changed the raw clone size objects stored in ApotcData objects, so all objects and pipelines used before this must be re-ran to be forwards compatible! This is technically a breaking change but the major version was not incremented since the fix should be relatively trivial.
• For vizAPOTC, RunAPOTC, APOTCPlot, fixed the subsetting arguments ... and extra_filter for cases where setting certain columns to only one level will erase extra data.
• Altered the ggplot object outputs of APOTCPlot and vizAPOTC to work with overlayLegend and removeLegend by introducing another element with a smaller size ApotcData object, and layers are now either named with an empty string or a layer label. Leftover ggplot objects from previous versions will have to be updated by re-running that command (APOTCPlot/vizAPOTC) that generated them.
• Fixed the functionality of the new_clone_scale_factor argument in AdjustAPOTC to guarantee it is a true rescaling of the clone scale factor, and the internally estimated cluster radii will correspondingly be modified to work with potential repulsion.
• Circles on legends of clonal expansion plots will now have the same linetype as the rest of the circles in a plot generated by APOTCPlot/vizAPOTC, whereas before they were forced to be blank.
• Legend background is now a single geom_rect annotation with a black border instead of a white rectangle stacked on top of a black rectangle.
• Many fixes to the behavior of AdjustAPOTC