Version: 2.19.4 Text: Removed #include from the C script, as this is not supported anymore, and I don't think we actually still used it. Version: 2.19.3 Text: Attempt to fix git issue with double file name Version: 2.19.2 Text: In NewData, only give warning messages when paramter in fsom object is TRUE Version: 2.13.16 Text: Changed input of metacluster parameter in Plot1DScatters to character Version: 2.13.15 Text: Added parameter to change axis and title labels font size to Plot2DScatters Version: 2.13.15 Text: Changed input of metacluster parameter in Plot2DScatters to character Version: 2.13.14 Text: Depricated PlotFileScatters (added to CytoNorm) Version: 2.13.14 Text: Aligned the x-axis labels to the top in PlotFileScatters Version: 2.13.13 Text: Changed TestOutliers function Version: 2.13.12 Text: Added PlotMFIHeatmap function Version: 2.13.12 Text: Changed heatmap in FlowSOMmary to PlotMFIHeatmap output Version: 2.13.11 Text: Added NewData parameter options to GetFeatures Version: 2.13.11 Text: Added warnings to NewData Version: 2.13.10 Text: Moved table overviews in FlowSOMmary to the end Version: 2.13.9 Text: Added Plot1DScatters function Version: 2.13.8 Text: Added ToScale option to readInput Version: 2.13.7 Text: Replaced geom_text with annotate in FlowSOMmary Version: 2.13.6 Text: Added (...) parameter to readInput to give to read.FCS Version: 2.13.5 Text: .data$ added to MajorityLabels function Version: 2.13.4 Text: Backgroundcolours are now updated with equalNodeSize Version: 2.13.3 Text: Added GetMajorityLabels function Version: 2.13.2 Text: Added (...) parameter to PlotFileScatter to give to read.FCS Version: 2.11.1 Text: Made GetFlowJoLabels more efficient Version: 2.9.3 Text: Added the option to adapt background size in PlotFlowSOM Version: 2.9.2 Text: Version bump Version: 2.9.2 Text: Small adaptations to make the GetFlowJoLabels function more robust Version: 2.7.10 Text: Fixed colored metacluster centers when using Plot2DScatters Version: 2.7.9 Text: Adapted documentation of readInput and FlowSOM. It can also use a matrix with column names Version: 2.7.8 Text: Added PlotOutliers and documentation Version: 2.7.7 Text: Updates to TestOutliers Version: 2.7.5 Text: Edited PlotManualBars so that it shows percentages of cells Version: 2.7.5 Text: Edited PlotDimRed so that it optionally uses scattermore if it installed Version: 2.7.4 Text: AggregateFlowFrames can now also resample if more cells are asked for than available in the fcs files. Default stays FALSE, taking at most the number of cells in the fcs file Version: 2.7.2 Text: Version bump to align with Bioconductor Version: 2.7.2 Text: Update for aggregateFlowFrames for nices handling of iterative aggregation (+ according visualisation in FlowSOMmary). AggregateFlowFrames will now introduce 0 values if a channel is not present in one of the fcs files. If channels is not provided as an argument, the channels of the first file are used. Version: 2.7.2 Text: Added support for abbrevations in PlotDimRed "colorBy". Version: 2.7.2 Text: Return 0 instead of NA in case of an empty cluster in GetCounts/GetPercentages Version: 2.5.6 Text: Reversed PlotDimred back to scattermore instead of geom_hex. Uses geom_point if scattermore is not available. Version: 2.5.6 Text: Added support for custom colors and limits in PlotDimRed Version: 2.5.5 Text: AddAnnotation now works correctly after using UpdateMetaclusters. The function also works slightly different. See examples. Version: 2.5.5 Text: Fixed issue with wrong coloring in PlotDimRed Version: 2.5.4 Text: percentage_positives in GetFeatures now works with a FlowSOM with updated metacluster labels Version: 2.5.3 Text: Bugfix in GetChannels Version: 2.5.2 Text: Bugfixes to pass BioConductor check Version: 2.5.2 Text: Bugfixes in Plot2DScatters: when ggpointdensity is not installed, normal ggplot colors are used Version: 2.5.2 Text: ParseNodeSize is now exported Version: 2.5.1 Text: Version bump to get the same version as on BioConductor Version: 2.5.1 Text: Changed yMargin parameter in PlotFileScatters to yLim for consistency Version: 2.5.1 Text: Added possibility to use abbrevations in GetFeatures, GetCounts, GetPercentages, PlotFileScatters, PlotDimRed, ParseQuery, Plot2DScatters and PlotNumbers Version: 2.5.1 Text: Moved UpdateFlowSOM to 0_FlowSOM.R Version: 2.5.1 Text: Changed examples in PlotFlowSOM, PlotVariable and PlotStars Version: 2.5.1 Text: Fixed issues from check: deleted examples with GetFlowJoLabels and used a csv instead, changed geom_scattermore to geom_hex for less dependencies. Moved packages to Suggest instead of Import. Version: 2.5.1 Text: ParseNodeSize is now exported Version: 2.1.38 Text: Added possibility to provide a seed when using metaClustering_hclust, metaClustering_kmeans or metaClustering_som Version: 2.1.37 Text: Added possibility to provide additional arguments to the read.FCS function in SaveClustersToFCS() function Version: 2.1.37 Text: PlotFileScatters now accepts other File ID columns, not anymore stricted to "File" Version: 2.1.36 Text: Added a warning when using "backgroundColor" instead of "backgroundColors" in PlotStars Version: 2.1.36 Text: Clusters centers in Plot2DScatters is now colored the same as the cluster cells when using manual colors Version: 2.1.35 Text: Added a warning in UpdateDerivedValue when using FlowSOM on an FCS with NA value Version: 2.1.34 Text: Happy Holidays! Version: 2.1.34 Text: Edited documentation of Plot2DScatters ("indices of clusters/metaclusters") Version: 2.1.34 Text: Outlier counts are also returned as attributes when extracting percentages with GetFeatures Version: 2.1.33 Text: Title of Plot2DScatters now gives all the (meta)clusters instead of just one Version: 2.1.33 Text: Added warning when wrong manual colors are used in Plot2DScatters Version: 2.1.33 Text: Added the ability to use markers and/or channels in Plot2DScatters Version: 2.1.33 Text: Added GetClusterPercentagesPositives and GetMetaclusterPercentagesPositives to FlowSOM CheatSheet Version: 2.1.33 Text: Edited text from GetFeatures on cheatsheet Version: 2.1.32 Text: Add marker outliers in TestOUtliers function Version: 2.1.32 Text: Add mad calculation in UpdateDerivedValues function Version: 2.1.31 Text: In NewData, the new FlowSOM object gets prettyColnames from the old one Version: 2.1.30 Text: GetFeatures can now return % of positive cells per channel for each cluster or metacluster, see parameters type and positives_cutoff Version: 2.1.30 Text: New exported function GetClusterPercentagesPositive Version: 2.1.30 Text: New exported function GetMetaclusterPercentagesPositive Version: 2.1.29 Text: Update documentation Version: 2.1.28 Text: Added height and width parameter to PlotFileScatters Version: 2.1.28 Text: Fixed bug in PlotFileScatters Version: 2.1.27 Text: Fixed typos and more consistent spelling Version: 2.1.26 Text: Adapted GetMetaclusterCVs function so that it works after using UpdateMetaclusters Version: 2.1.26 Text: Fixed typos Version: 2.1.25 Text: Adapted PlotManualBars function so that it works after using UpdateMetaclusters Version: 2.1.24 Text: Added UpdateMetaclusters function, removed RelabelMetaclusters, ReassignMetaclusters and Reordermetaclusters functions. Version: 2.1.24 Text: Updated CheatSheet Version: 2.1.24 Text: Added code from UpdateDerivedValues for metaclustersMFIs to UpdateFlowSOM Version: 2.1.23 Text: Added checkNames = FALSE in MetaclusterMFIs Version: 2.1.22 Text: Reordered code in UpdateDerivedValues, RelabelMetaclusters, ReorderMetaclusters and ReassignMetaclusters. Version: 2.1.21 Text: Added ReorderMetaclusters, to reorder the metacluster levels. Version: 2.1.20 Text: Updated PlotManualBars, Plot2DScatters and FlowSOMmary so that it works with relabeled metaclusters. Version: 2.1.19 Text: AggregateFlowFrames accepts channels and markers Version: 2.1.19 Text: AggregateFlowFrames now gives a warning when files do not contain the same number of channels Version: 2.1.19 Text: AggregateFlowFrames now gives warnings when files do not contain the same markers Version: 2.1.19 Text: Bugfix in AggregateFlowFrames now works when one channel is given Version: 2.1.19 Text: Bugfix in PlotFileScatters now works when one channel is given Version: 2.1.19 Text: Added silent parameter in PlotFileScatters to stop messages Version: 2.1.19 Text: PlotFileScatters supports channels and markers now Version: 2.1.19 Text: Add info to FlowSOM object: date when flowSOM object is made, FlowSOM verion and arguments given to FlowSOM call Version: 2.1.19 Text: Fixed bug in PlotManualBars Version: 2.1.19 Text: Added silent parameter in NewData. GetFeatures' silent parameter now also surpresses message from NewData (more concrete: ReadInput) Version: 2.1.17 Text: Added ReassignMetaclusters, to rename or split metaclusters Version: 2.1.17 Text: Fixed issue where a lot of warnings were printed in FlowSOMmary Version: 2.1.17 Text: PlotFilescatters now makes filenames unique if they are not and the function now works with output of AggregateFlowFrames Version: 2.1.16 Text: PlotManualBars allows input of NewData function Version: 2.1.15 Text: Fixed warnings with ggtexttable in FlowSOMmary Version: 2.1.13 Text: Added RelabelMetaclusters Version: 2.1.13 Text: PlotFileScatters now has a parameter to change the y-axis label to markers and/or channels (yLabel) Version: 2.1.13 Text: Now TRUE/FALSE vector is accepted as input in GetMarkers/GetChannels Version: 2.1.11 Text: Added example to AddAnnotation Version: 2.1.11 Text: Added example to NClusters, NMetaclusters Version: 2.1.11 Text: Changed examples that used fsom to flowSOM.res Version: 2.1.11 Text: Added textColor and textSize to AddLabels and PlotNumbers, PlotLabels Version: 2.1.11 Text: PlotNumbers can plot clusters and metaclusters with parameter "level" Version: 2.1.11 Text: In GetFeatures, the population parameter is changed to level Version: 2.1.11 Text: Added GetCounts and GetPercentages to get counts or percentages respectively per cluster or metacluster Version: 2.1.11 Text: FlowSOMmary doesn't crash anymore with a column with the same values in heatmap Version: 2.1.11 Text: Included a print function for FlowSOM class Version: 2.1.11 Text: Fixed bug in PlotManualBars Version: 2.1.11 Text: PlotMarker also accept multiple markers now Version: 2.1.8 Text: Solved issue when matrix with no column was given to the SOM function Version: 2.1.5 Text: Scale parameter in FlowSOM function defaults to FALSE. Version: 2.1.5 Text: FlowSOM wrapper function now returns the FlowSOM object instead of a list containing the FlowSOM object and a metaclustering Version: 2.1.5 Text: 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. Version: 2.1.5 Text: If you want to reuse FlowSOM objects generated by previous versions, you can use the UpdateFlowSOM function. Version: 2.1.5 Text: FlowSOM now uses nClus = 10 as default instead of maxMeta = 10 Version: 2.1.5 Text: 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, ... Version: 2.1.5 Text: GetChannels/GetMarkers can now also take a FlowSOM object as input instead of a flowFrame. New functions: Version: 2.1.5 Text: To easily generate a clear summary of the model with multiple plots, you can now use the FlowSOMmary function, which creates a pdf file. Version: 2.1.5 Text: GetFeatures allows to map new files (internally using the NewData function) and can return cluster counts, percentages and MFI values for each individual sample. Version: 2.1.5 Text: PlotFileScatters can be useful to get an overview of potential batch effects before running the FlowSOM algorithm Version: 1.15.5 Text: Removed dependency on flowUtils, replaced by flowWorkspace. This also included a filename change of lymphocytes.fcs to 68983.fcs Version: 1.15.5 Text: Included Version: 1.15.4 Text: Fix bug when aggregating files with different column orders Version: 1.15.4 Text: Fix bug in PlotNode which failed when there were any clusters with no cells assigned. Version: 1.15.3 Text: Fix bug when mapping an fcs file with different columns (eg. no "File" columns as in the aggregated file used for training) Version: 1.15.3 Text: Allow multiple repeated aggregations with the AggregateFlowframe function Version: 1.13.11 Text: The ReadInput function can now also take a matrix as input. Version: 1.13.11 Text: Made input of the NewData function more general (can now take any input of the ReadInput function). Version: 1.13.11 Text: 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. Version: 1.13.11 Text: Fixed the bug that only the first file-specific compensation matrix was taken into account in the ReadInput function. Version: 1.13.10 Category: Add rownames to the MFI results Text: Version: 1.13.9 Text: 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. Version: 1.13.8 Text: added get_markers and get_channels functions for easier access Version: 1.13.8 Text: added PlotOverview2D function, which gives an overview of multiple PlotCluster2D plots. Version: 1.13.7 Text: Background circles scale with the actual node size Version: 1.13.7 Text: Possible to choose at which level warnings for bad mappings to cluster are generated (mean + x * sd), default changed from 3 to 4 Version: 1.13.7 Text: If more than 10 background values, split legend in multiple columns Version: 1.13.6 Text: Transposed the metaclusterMFI result!! Version: 1.13.2 Text: Added a MetaclusterCVs function to get coefficient of variation for the metaclusters Version: 1.13.1 Text: Added a warning when cells mapped with the NewData function seem further away from their cluster center then normal Version: 1.10.3 Text: Bugfix in PlotGroups Version: 1.10.1 Text: Updates to the PlotGroups function: - Changed the default from fold change (tresh) to p-value (p_tresh) - Make use of adjusted p-values Version: 1.10.1 Text: Added a check on the input format of the codes parameter in the SOM function Version: 1.1.0 Category: NEW FEATURES Text: Cleaned up some code Version: 0.99.4 Category: NEW FEATURES Text: Extra functionality to differentiate between groups of samples Version: 0.99.0 Category: NEW FEATURES Text: First version of the package