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 - specified by transform = - 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

######################################################### load single file
workspace = "workspace.wsp"
sample = "workspace/data.fcs"
data,labels,groups,gating = load(sample; workspace=workspace)

######################################################### load multiple files with different channel names
channelMap = Dict([

    "FJComp-355 820_60-A"=>"CD4",
    "FJComp-355 670_30-A"=>"CD4",
    "Foxp3-IgM"=>"Foxp3",
    ...
])

pattern = glob"workspace/*.fcs"
data,labels,groups,gating = load(pattern; workspace=workspace, channelMap=channelMap)