CHANGES IN VERSION 2.1.16 (2021/04/13) - Bioconductor 1.99.7
--------------------------------------
o PlotManualBars allows input of NewData function

CHANGES IN VERSION 2.1.15 (2021/04/13)
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o Fixed warnings with ggtexttable in FlowSOMmary

CHANGES IN VERSION 2.1.13 (2021/04/06)
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o Added RelabelMetaclusters 
o PlotFileScatters now has a parameter to change the y-axis label to markers
  and/or channels (yLabel)
o Now TRUE/FALSE vector is accepted as input in GetMarkers/GetChannels

CHANGES IN VERSION 2.1.11 (2021/03/03)
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o Added example to AddAnnotation
o Added example to NClusters, NMetaclusters
o Changed examples that used fsom to flowSOM.res
o Added textColor and textSize to AddLabels and PlotNumbers, PlotLabels
o PlotNumbers can plot clusters and metaclusters with parameter "level"
o In GetFeatures, the population parameter is changed to level
o Added GetCounts and GetPercentages to get counts or percentages respectively 
  per cluster or metacluster
o FlowSOMmary doesn't crash anymore with a column with the same values in 
  heatmap
o Included a print function for FlowSOM class
o Fixed bug in PlotManualBars
o PlotMarker also accept multiple markers now


CHANGES IN VERSION 2.1.8 (2020/11/19)
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o Solved issue when matrix with no column was given to the SOM function


CHANGES IN VERSION 2.1.5 (2020/11/19)
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o Scale parameter in FlowSOM function defaults to FALSE.
o FlowSOM wrapper function now returns the FlowSOM object instead of a list 
  containing the FlowSOM object and a metaclustering
o The metaclustering is now found as an element in the flowSOM object. Also the 
  number of metaclusters and the MFI values are stored and can be accessed by
  the NMetaclusters() and GetMetaclusterMFIs() functions.
o If you want to reuse FlowSOM objects generated by previous versions,
  you can use the UpdateFlowSOM function.
o FlowSOM now uses nClus = 10 as default instead of maxMeta = 10
o FlowSOM now makes use of ggplot2 for plotting. PlotFlowSOM provides the 
  main structure, and has parameters to adapt nodeSize, view (grid, MST or some
  own layout matrix), ... PlotStars etc build on this by adding additional
  layers to the ggplot object. This also allows to easily incorporate multiple
  plots in all layout-tools such as ggarrange, cowplot, patchwork, ...
o GetChannels/GetMarkers can now also take a FlowSOM object as input instead of
  a flowFrame.
New functions:
o To easily generate a clear summary of the model with multiple plots, you
  can now use the FlowSOMmary function, which creates a pdf file.
o GetFeatures allows to map new files (internally using the NewData function) 
  and can return cluster counts, percentages and MFI values for each individual
  sample.
o PlotFileScatters can be useful to get an overview of potential batch effects
  before running the FlowSOM algorithm

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)
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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
