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