NEWS

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DepecheR 1.21.3 (2024-06-21)

• Minor bugs affecting the special case of one defining marker and two clusters.

DepecheR 1.21.2 (2024-06-14)

• Correction of the number of used neighbors in neighSmooth function.

DepecheR 1.19.9 (2024-01-15)

• Bug fixes

DepecheR 1.17.8 (2024-01-15)

• dAllocate test changed, to accomodate the changes below, where the function is no longer included as one of the user fuctions of the package.

DepecheR 1.17.7 (2024-01-05)

• Updates to the neighSmooth function, first to increase the speed of the K- means clustering, and second to allow for external principal component analysis and clustering, which makes bootstrapping easier.

DepecheR 1.17.6 (2023-12-21)

• The dAllocate standalone function is removed as a separate export. If a large dataset should be clustered, use the samplingSubset flag to control which events that are used to build the model, if for example multiple donors with different cell numbers should be given the same influence.

DepecheR 1.17.5 (2023-11-09)

• Set.seed belatedly introduced into test functions to avoid the uncommon but repeated slight numeric errors in the tests.
• dAllocate bug removed.
• Small note removal cosmetics without any functional impact.

DepecheR 1.17.4 (2023-08-14)

• Adding collapse package to the description file.
• Correction of the generateSparseData function.
• Set.seed removed from two places and now non-present in the package.

DepecheR 1.17.3 (2023-07-26)

• Correction to groupProbPlot, as the last version threw out the most significant cells.

DepecheR 1.17.2 (2023-07-14)

• Correction to scale in groupProbPlot.

DepecheR 1.17.1 (2023-07-13)

• A mode option is added to the neighSmooth function.
• The scale of the groupProbPlot output is corrected, to -100, over 50 to 100.

DepecheR 1.11.4

• sPLSDA function testing excluded from BioConductor, as it works locally, but fails at BioConductor.

DepecheR 1.11.3 (2022-03-12)

• Bug fix in dColorPlot affecting character vectors and factors used as input.

DepecheR 1.11.2 (2022-03-11)

• Searching for unidentified bug in test for dSlsda function.

DepecheR 1.11.1 (2022-03-05)

• Bug fix in dColorPlot, solving problems with individual continuous vectors
• microClust, an internal function, has been updated to include the counting of donors in addition to median and mean calculations among the neighbors.
• The addition of nUniqueNeihgDons, in conjunction to the aforementioned change to the microClust function.
• Minor updates to dSplsda function testing, to hopefully remove the problem of intermittent problems in the testing on the Linux plaform.

DepecheR 1.9.1 (2021-10-16)

• depecheCoFunction updated to remove traces of the old dAllocate functionality

DepecheR 1.7.2 (2021-03-25)

• Major internal changes to the depeche function, with two user consequences: o The dualDepeche option is deprecated, as it made the function very heavy to maintain and was not flexible enough to be of great use. o The interface to dAllocate is much improved, allowing for smooth allocation of new data to an established model, which makes large dualDepeche runs, constructed outside of the function, possible in a more versatile way than previously.

DepecheR 1.7.1 (2021-02-02)

• Adding the option of not scaling the data within the depeche function
• Condensing the code for the depeche scaling procedure

DepecheR 1.5.4 (2020-09-17)

• Correction of the information about the content of the output from depeche.

DepecheR 1.5.3 (2020-07-02)

• Correcting the p-adjustments, so that it in fact uses Benjamini-Hochberg, and
• not the more conservative Hochberg, as default.

DepecheR 1.5.2 (2020-06-05)

• Introducing samplingSubset in the depeche function
• Bug fixes in dOptPenalty
• Small text updates to main vinjette and examples, without code implications.

DepecheR 1.5.1 (2020-05-18)

• Introduction of neighSmooth - a generalization of groupStatPlot.
• Bug fix and simplification of dOptPenalty termination criteria.
• Re-tidying of the code base.

DepecheR 1.3.3 (2020-03-18)

• Hiearchical clustering and ordering of the columns in the Cluster_centers heatmap from depeche.
• Note fixed regarding the use of ::: in GroupStatPlot

DepecheR 1.3.2 (2020-02-05)

• Bug fix in groupProbPlot solving issues when the cell number is low.
• Update of dWilcox.

DepecheR 1.3.1 (2019-12-05)

• Vinjette changes o Introduction of a vinjette for the groupProbPlot function. o Fixing a minor bug in the general vinjette.

DepecheR 1.1.9 (2019-10-06)

• Two changes making package more BioConductor compliant: o Introduction of a "Installation" and a "Session info" slot in the vinjette o Formatting change of this NEWS file.

DepecheR 1.1.8 (2019-09-12)

• Bug fixes. True also for last version.

DepecheR 1.1.6 (2019-09-12)

• Adding export option for the vector created by groupProbPlot
• Correcting dColorPlot so that it can take a hex color vector as input, and
• keep the colors.
• Adding a test for groupProbPlot.
• Minor bug fixes for groupProbPlot.
• Small edits to the vinjette, to clarify that umap is preferred over tSNE and
• that dViolins currently does not fully support plotting of CyTOF data due to
• its sparsity.

DepecheR 1.1.5 (2019-08-07)

• 4x speedup of the new groupProbPlot.
• Proper citations of the MixOmics package, that the dSplsda function uses
• heavily.
• Bug fixes of the groupProbPlot.

DepecheR 1.1.4 (2019-07-30)

• A brand new function is added! Here, the user can get single-cell resolution
• on which group of two that a cell is more probable to belong to. See docs for
• further information. Highly recommended to test!
• Internal c++ test corrected by external contribution by Zimoun, which we are
• most grateful for.

DepecheR 1.1.3 (2019-06-28)

• dResidualPlot bug making colors sometimes represent the wrong group fixed.

DepecheR 1.1.2 (2019-06-28)

• Fixing the dColorPlot and the dDensityPlot functions, so that original names
• in character vectors and factors are correctly displayed.

DepecheR 0.99.31 (2019-03-13)

• dColorPlot and dDensity plot simplified, in that it is now possible to add
• just a vector of any kind, and it will be returned as colors.
• A colorScale alternative, linking to dColorVector has been added to the above.
• A new legend has been added to dColorPlot.
• The options createDirectory and directoryName have been removed from all
• visualization functions and have been replaced by plotDir.
• The different "name" arguments for plots have been streamlined to be called
• plotName in all instances, to avoid using base function names for objects.
• The testData dataset has been made smaller, to increase example execution time
• and diminish pacakge size.
• dViolins completely worked over. Now, assymetrical violin plots are generated,
• leading to a more succinct result.
• Responses to all issues raised by BioConductor reviewer.
• Bug fix in dual depeche

DepecheR 0.99.30 (2019-02-18)

• dViolins completely worked over. Now, assymetrical violin plots are generated,
• leading to a more succinct result.
• Responses to all issues raised by BioConductor reviewer.
• Bug fix in dual depeche

DepecheR 0.99.24 (2019-01-24)

• Technical, internal tests have been made more efficient.
• Redundant and time consuming examples have been given a dontrun command.
• No changes to user functions.

DepecheR 0.99.20 (2019-01-23)

• Selecting the number of used cores made more Windows-friendly.

DepecheR 0.99.13 (2019-01-18)

• Package size made considerably smaller.

DepecheR 0.99.9 (2019-01-15)

• The figure files connected to the vinjette have been moved out of the package
• to a separate github directory. This will reduce the package size
• significantly.

DepecheR 0.99.3 (2019-01-15)

• No errors or warnings in BiocCheckGitClone after removal of .Rapp.history

DepecheR 0.99.1 (2019-01-14)

• C++ code reorganized, making package considerably smaller after build.
• Package now passes both CMD check and BiocCheck without errors or warnings.

DepecheR 0.81.4 (2019-01-11)

• Multicore feature made functional for dColorPlot, increasing execution speed.

DepecheR 0.81.3 (2019-01-11)

• CMD check, test_that BiocCheck all pass.

DepecheR 0.81.2 (2019-01-11)

• BiocCheck() compliance increased: o seq functions used instead of : o vapply is used instead of sapply.

DepecheR 0.81.1 (2019-01-10)

• A vignette has been created.
• A visual bug, making the colors reversed in the residual plot function
• compared to the dWilcox and DSplsda functions has been removed.
• Formatting to satisfy the BioConductor criteria has been added.
• Tests have been adapted to work after reformatting
• No actual changes have been added to the code.

DepecheR 0.80.3 (2019-01-09)

• This is the first time the NEWS file is present.
• For all previous changes, and those are hundreds, see the git push messages.