Changes in version 1.11.4/5 (2022-03-17/27) + sPLSDA function testing excluded from BioConductor, as it works locally, but fails at BioConductor. Changes in version 1.11.3 (2022-03-12) + Bug fix in dColorPlot affecting character vectors and factors used as input. Changes in version 1.11.2 (2022-03-11) + Searching for unidentified bug in test for dSlsda function. Changes in version 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. Changes in version 1.9.1 (2021-10-16) + depecheCoFunction updated to remove traces of the old dAllocate functionality Changes in version 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. Changes in version 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 Changes in version 1.5.4 (2020-09-17) + Correction of the information about the content of the output from depeche. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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 Changes in version 1.3.2 (2020-02-05) + Bug fix in groupProbPlot solving issues when the cell number is low. + Update of dWilcox. Changes in version 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. Changes in version 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. Changes in version 1.1.8 (2019-09-12) + Bug fixes. True also for last version. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 1.1.3 (2019-06-28) + dResidualPlot bug making colors sometimes represent the wrong group fixed. Changes in version 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. Changes in version 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 Changes in version 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 Changes in version 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. Changes in version 0.99.20 (2019-01-23) + Selecting the number of used cores made more Windows-friendly. Changes in version 0.99.13 (2019-01-18) + Package size made considerably smaller. Changes in version 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. Changes in version 0.99.3 (2019-01-15) + No errors or warnings in BiocCheckGitClone after removal of .Rapp.history Changes in version 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. Changes in version 0.81.4 (2019-01-11) + Multicore feature made functional for dColorPlot, increasing execution speed. Changes in version 0.81.3 (2019-01-11) + CMD check, test_that BiocCheck all pass. Changes in version 0.81.2 (2019-01-11) + BiocCheck() compliance increased: o seq functions used instead of : o vapply is used instead of sapply. Changes in version 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. Changes in version 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.