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Process a flowjo workspace file

Source: R/gating.R
getFlowJoLabels.Rd

Reads a flowjo workspace file using the flowWorkspace library and returns a vector with a label for each cell of a flowFrame from a set of specified gates. If the flowFrame was generated from several files (contains a 'File' column containing a file index), then the groups should contain the group name to apply for each of these files/samples

Usage

getFlowJoLabels(
  ff,
  wspFile,
  groups = "All Samples",
  sampleInGroups = NULL,
  cellTypes = NULL,
  defaultCellTypes = c("leaves", "all"),
  specialCharsInChannels = c("/"),
  FlowJoCharsinChannels = c("_"),
  withFJv10TimeCorrection = TRUE,
  ...
)

Arguments

ff

a flowCore::flowFrame

wspFile

a flowjo workspace

groups

vector of flowjo groups to parse from the flowjo workspace (i.e. one for each sample/file used to generate the flowFrame). Default c("All Samples")

sampleInGroups

vector of flowjo sample index in group to use from the flowjo workspace (i.e. one for each sample/file used to generate the flowFrame). If not provided, will start from 1 in each group and increment. Default NULL.

cellTypes

vector of flowJo gate nodes to parse (should be common to all groups!). Default NULL then uses either all leaf node from first group, or all gates from first group, depending on 'defaultCellTypes'.

defaultCellTypes

if cellTypes are not specified, than triggers the choice of either :

  • all leaf nodes ('leaves') (the default)

  • all nodes ('all')

specialCharsInChannels

vector of special char litterals that are replaced in FlowJo workspace

FlowJoCharsinChannels

vector of new char litterals to be applied in FlowJo workspace

withFJv10TimeCorrection

if TRUE (default), applies a time correction to cope with a bug in flowJo 10.0. Should be kept TRUE with FloJo v>10.0 if time channel is used in gating.

Since FlowJo v10, time channel is read differently from fcs files (see https://docs.flowjo.com/flowjo/experiment-based-platforms/kinetics/ how-flowjo-handles-time/). The resulting scale transformation on the time channel is normally stored in the corresponding tranformation gain parameter in the FlowJo workspace. However, somehow this gain parameter can be sometimes wrong in the .wsp file, and so the workaround consists in correcting the time channel values of the cytoset prior to gating, in order to have the gate labels calculated correctly.

...

Extra arguments passed to CytoML::flowjo_to_gatingset()

Value

a list with :

  • the first element ("matrix") is a matrix containing filtering results for each specified gate

  • the second element ("labels") is a vector which assigns one label to each cell. If no cell type correspond to a specific cell, than the keyword 'unlabeled' is assigned to this cell. If the cell belongs to several gates (meaning that the gates ar not disjoints), than this cell is assigned to the gate with the less matching cells.