Release Notes¶
Version 1.3.0: October 5, 2023¶
General:
- Updated dependencies alakazam >= 1.3.0, shazam >= 1.2.0, ggplot2 >= 3.4.0.
- Added a
locus
column to the package’s example data, to satisfy alakazam >= 1.3.0 requirements.
Version 1.2.1: September 21, 2022¶
Bug fixes:
-
Fixed a bug
defineClonesScoper
where the bulk clonal clustering was using light chain sequences. Now, light chain sequences are removed based on thelocus
information. If the columnlocus
does not exist, it is created withalakazam::getLocus(v_call)
. -
Fixed a bug in
defineClonesScoper
where thesplit_light
part of the algorithm was reanalyzing heavy chain v_calls and using this information to sometimes split clone_id groups into subgroups. Only light chain v_calls should be used for this. The bug could be observed in situations wherefirst=FALSE
and the ‘linker’ ambiguous heavy chain v_calls were left out of the same clone_id group because of the junction distance threshold. -
Fixed parallelization setup for
defineClonesScoper
.
General:
- Improved hierachical clustering performance.
Version 1.2.0: November 2, 2021¶
General:
- Updated dependencies to R >= 4.0, ggplot2 >= 3.3.4, dplyr >= 1.0, alakazam >= 1.2.0, and shazam >= 1.1.0.
- Changed the internal definition of degenerate characters from
N
to any characters except[ATCG]
.
Cloning:
- Added
fields
argument toidenticalClones
,hierarchicalClones
andspectralClones
to allow for data partitioning prior to clonal assignment. - Fixed a bug in the cloning functions causing an error in single-cell mode when the input data contains only heavy chains.
Version 1.1.0: August 10, 2020¶
- Fixed a bug in the clonal clustering methods causing TCR data to fail.
- Added support for single-cell data in the clonal clustering methods, which
are enabled by defining the optional
cell_id
column.
Version 1.0.1: May 24, 2020¶
- Fixed a fatal error in
identicalClones
,hierarchicalClones
andspectralClones
when specifyingnproc
> 1.
Version 1.0.0: May 15, 2020¶
Backwards Incompatible Changes:
- Changed default expected data format from the Change-O data format to the
AIRR Rearrangement standard. For example: where functions used the column
name
V_CALL
(Change-O) as the default to identify the field that stored the V gene calls, they now usev_call
(AIRR). That means, scripts that relied on default values (previously,v_call="V_CALL"
), will now fail if calls to the functions are not updated to reflect the correct value for the data. If data are in the Change-O format, the current default valuev_call="v_call"
will fail to identify the column with the V gene calls as the columnv_call
doesn’t exist. In this case,v_call="V_CALL"
needs to be specified in the function call. ExampleDb
converted to the AIRR Rearrangement standard and examples updated accordingly.- Split
defineClonesScoper
function to three functions:identicalClones
,hierarchicalClones
, andspectralClones
.
General:
- License changed to AGPL-3.
Cloning:
- Fixed a platform precision incompatibility bug which caused spectral cloning results to be non-reproducible across platforms.
- Added largest distance-to-nearest filter to clustering process.
Version 0.2.0: August 5, 2019¶
Deprecated:
- function
analyzeClones
is deprecated. The clonal analysis has been added to the main functiondefineClonesScoper
as an argumentanalyze_clones
. - the out put class is deprecated. Results would be reported as a list if
argument
analyze_clones
set to be true, otherwise a single dataframe is returned. plot_neighborhoods
from clonal analysis has been deprecated.neighborhoods
from clonal analysis has been deprecated.
General:
- New models,
hierarchical
for hierarchical-clustering based, andidentical
for clustering among identical junction sequences are added. - New method for spectral-clustering based model has been added through the
vj
in argumentmethod
.
Clonal analysis:
- Switched the meaning of the “inter” and “intra” labels in
calculateInterVsIntra
function. Now, “inter” is the label used to form distances that mean between clones, and “intra” is the label used to form distances that mean on the inside, within each clone. - Changed the
plotInterVsIntra
output from a density plot to a histogram. - Changed the way to calculate the effective threshold. Now, desntiy approach is used.
Version 0.1.0: October 4, 2018¶
Initial public release.