gszep/flowworkspace.jl

Load useful metadata from FlowJo workspace files such as gating strategies and sample groups

FlowWorkspace.jl

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.

Installation

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

Basic Usage

⚠️ 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)