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Changelog

Source: NEWS.md

APackOfTheClones 1.2.4

CRAN release: 2024-11-18

Additions

  • Update citation information as the tool has been published.

Changes

  • slightly improve README
  • Ensured all irrelevant files are not included in the package build to address CRAN submissions failures for the previous 2 patches.

APackOfTheClones 1.2.1

CRAN release: 2024-10-10

Additions

  • Add code of conduct and contributing guidelines in the package source code.
  • Add assertthat in imports.

Changes

  • The main change in this patch is a minor alteration in the circle packing algorithm that should result in packings acting slightly more consistent across different physical systems. This may result in slightly different circle placements in the clonal expansion plot, but the overall structure should remain the same. This is pretty much only noticeable in the case of extremely small testing datasets, which is why this is a patch version. However, it is very possible that the same seurat object will produce a slightly different packing than before.
  • updated citation information
  • Updated the combined_pbmc dataset to be up-to-date with the latest version of Seurat.
  • Spelling & minor fixes / updates to various functions, documentation.
  • Removed package startup deprecation message for returning users of version 0.1.x.
  • Removed the explicit magrittr dependency.

APackOfTheClones 1.2.0

CRAN release: 2024-04-16

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.

APackOfTheClones 1.1.0

CRAN release: 2024-04-05

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

APackOfTheClones 1.0.0

CRAN release: 2024-01-13

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

APackOfTheClones 0.1.4 (github release)

Additions

  • The clonal expansion plotting function now has a new optional argument reduction which now allows the user to choose which reduction the circle clonal clusters should be based on. Defaults to 'umap' but can now be changed to 'tsne' or 'pca' given that they have been ran already on the seurat object. The vignette has been updated accordingly as well
  • New CRAN badge showing date of latest release on README.md

Changes

  • Some testcases have been altered/fixed to pass CRAN’s R-CMD check
  • Package startup message has been improved

APackOfTheClones 0.1.3

CRAN release: 2023-07-16

Additions

  • clonal_expansion_plot now displays time elapsed if verbose = TRUE
  • There are now package startup messages

Changes

  • Many functions have been rewritten in C++, improving the circle packing runtime of clonal_expansion_plot 70 ~ 140 fold. For reference, for a dataset with around 2500 viable T cells, the runtime averages 0.1s

APackOfTheClones 0.1.2

CRAN release: 2023-05-09

Additions

  • Two new datasets previously in the test folder have now moved to \data and are available to users and can be called via data("mini_seurat_obj") and data("mini_clonotype_data").

Changes

  • Released package to CRAN.
  • Minor documentation changes to adhere to CRAN standards.

APackOfTheClones 0.1.1 (github release)

Additions

  • A preliminary user vignette can be viewed on the documentation website, but not locally.

Changes

  • An initial version of automated cluster repulsion is correctly implemented and the related arguments in clonal_expansion_plot has been “unlocked”.
  • Size legends are now correctly implemented, and the related arguments have also been “unlocked” in clonal_expansion_plot.
  • Function documentation and the README in general has been slightly improved. (automatically updated on the pkgdown website)

APackOfTheClones 0.1.0 (github release)

Initial semi-stable release. The main functions of the package are working with their default parameters. The package currently exports three functions:

  • integrate_tcr
  • count_clone_sizes
  • clonal_expansion_plot

All of which have documentation, including on the documentation site.

Currently, Automated cluster repulsion uses a highly flawed mathematical formula loosely based on force directed graph drawing techniques, the resulting plots are not presentable and the function has been disabled temporarily