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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[v1 Release Candidate]

v1 will be the first stable release of the CellEngine R toolkit and has several breaking changes compared to the pre-release version.

Added

  • createCompensation() function
  • getCompensation() function
  • updateCompensation() function
  • deleteCompensation() function
  • All functions now consistently accept byName() expressions for any ID parameter.
  • Support for transfers to S3 to getEvents()
  • PER_FILE compensation constant
  • Support for geometricMean as a statistics value in getStatistics().
  • Support for layout argument in getStatistics().

Changed

  • Breaking Failed API requests will now stop instead of warn.
  • Breaking getEvents() now uses check.names=FALSE, so data.frame column names will be identical to the parameter names found in the FCS file. For example, "CD4 (Ax647-A)" will no longer be converted to "CD4..Ax647.A.".
  • Breaking getEvents() now defaults to headerQ=TRUE, so data.frames will have column names by default now.
  • Breaking In getEvents(), the argument clamp_q was renamed to clampQ.
  • Breaking The default for the createPopulation parameter of gate creation functions was changed to is.null(fcsFileId).
  • Breaking getCompensations() now returns a list of lists, with the spillMatrix formatted as a matrix.
  • Breaking All functions now return lists instead of data.frames. (In the future, the lists may be changed to S3 classes.)
  • Breaking The xVertices and yVertices parameters of createPolygonGate are replaced with vertices=list(c(x1, y1), c(x2, y2), c(x3, y3)).
  • Breaking The create__Gate() functions previously had two parameters for specifying the FCS file for tailoring (fcsFileId and fcsFile) and two parameters for specifying the parent population (parentPopulationId and parentPopulation), with the latter parameters performing a lookup by name. To be consistent with the rest of the toolkit, fcsFile and parentPopulation have been removed. Instead, use byName() expressions, e.g. createRectangleGate(..., fcsFileId=byName("Sample1.fcs"), parentPopulationId=byName("CD3+"), ...).
  • createQuadrantGate() and createSplitGate() accept either createPopulation, singular, for consistency with other create__Gate functions; or createPopulations, plural, to accurately reflect the behavior.
  • getStatistics(fcsFileIds=NULL, ...) should return statistics for all non-control FCS files.
  • getStatistics() should support percentOf=c("PARENT").
  • getStatistics(populations=c("pop1", "pop2", ...)) should return statistics for all specified populations.

Removed