CHANGES IN VERSION 1.15.5 (2019/06/11) -------------------------------------- o Removed dependency on flowUtils, replaced by flowWorkspace. This also included a filename change of lymphocytes.fcs to 68983.fcs o Included CHANGES IN VERSION 1.15.4 (2019/05/17) -------------------------------------- o Fix bug when aggregating files with different column orders o Fix bug in PlotNode which failed when there were any clusters with no cells assigned. CHANGES IN VERSION 1.15.3 (2019/04/08) -------------------------------------- o Fix bug when mapping an fcs file with different columns (eg. no "File" columns as in the aggregated file used for training) o Allow multiple repeated aggregations with the AggregateFlowframe function CHANGES IN VERSION 1.13.11 (2018/09/26) -------------------------------------- o The ReadInput function can now also take a matrix as input. o Made input of the NewData function more general (can now take any input of the ReadInput function). o Included a TestOutliers function which checks the average distance of the cells to the cluster centers (using the median and MAD measures) and returns how many cells seem to be further then expected from the cluster center. o Fixed the bug that only the first file-specific compensation matrix was taken into account in the ReadInput function. CHANGES IN VERSION 1.13.10 (2018/09/18) -------------------------------------- Add rownames to the MFI results CHANGES IN VERSION 1.13.9 (2018/09/13) -------------------------------------- Added a keepOrder parameter to the AggregateFlowFrames function. If TRUE, the cells of the random subsample will be ordered in the same way as they were originally ordered in the file. Default = FALSE for backwards compatability. This will be especially useful if the whole file is selected in the subsample, in which case indices keep corresponding to the original ones. Also included the bugfix by Stu Blair to propagate the main parameter of the plotnumbers function to igraph. CHANGES IN VERSION 1.13.8 (2018/08/29) -------------------------------------- o added get_markers and get_channels functions for easier access o added PlotOverview2D function, which gives an overview of multiple PlotCluster2D plots. CHANGES IN VERSION 1.13.7 (2018/08/23) -------------------------------------- o Background circles scale with the actual node size o Possible to choose at which level warnings for bad mappings to cluster are generated (mean + x * sd), default changed from 3 to 4 o If more than 10 background values, split legend in multiple columns CHANGES IN VERSION 1.13.6 (2018/08/21) -------------------------------------- o Transposed the metaclusterMFI result!! CHANGES IN VERSION 1.13.2 (2018/08/20) -------------------------------------- o Added a MetaclusterCVs function to get coefficient of variation for the metaclusters CHANGES IN VERSION 1.13.1 (2018/04/09) -------------------------------------- o Added a warning when cells mapped with the NewData function seem further away from their cluster center then normal CHANGES IN VERSION 1.10.3 (2018/04/09) -------------------------------------- o Bugfix in PlotGroups CHANGES IN VERSION 1.10.1 (2017/01/03) -------------------------------------- o Updates to the PlotGroups function: - Changed the default from fold change (tresh) to p-value (p_tresh) - Make use of adjusted p-values o Added a check on the input format of the codes parameter in the SOM function CHANGES IN VERSION 1.1.0 (2015/07/06) -------------------------------------- NEW FEATURES o Cleaned up some code CHANGES IN VERSION 0.99.4 (2015/03/17) -------------------------------------- NEW FEATURES o Extra functionality to differentiate between groups of samples CHANGES IN VERSION 0.99.0 (2014/10/15) -------------------------------------- NEW FEATURES o First version of the package