This package provides for loading and parsing of FlowJo Workspace files in pure Julia. The gating strategy is parsed as a DiMetaGraph and group membership as Dict. Together with GigaSOM.jl this metadata can be used to generate event-level labels for FCS datasets.

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Type ] add FlowWorkspace and then hit ⏎ Return at the REPL. You should see pkg> add FlowWorkspace.

Basic Usage

:warning: FCS files under a workspace must have unique names. This limitation will be removed in future versions

The load method returns a tuple of three DataFrames and one Dict:

  • data transformed fluorescence values for each event
  • labels boolean telling us which events have been gated
  • groups booleans telling us which group each event belongs to
  • gating Dictionary of graph representations of each gating strategy
using FlowWorkspace
data,labels,groups,gating = load("workspace.wsp"; files="*.fcs", cols=:setequal)