Add FileIO.jl
integration for flow cytometry FCS files.
Stable release | Repo status |
---|---|
FCS files can be loaded by using the FileIO interface.
julia> using FileIO
julia> flowrun = load("example.fcs")
FCS.FlowSample{Float32}
Machine: LSRFortessa
Begin Time: 14:12:03
End Time: 14:12:25
Date: 17-MAR-2017
File: Specimen_001_Tube_002_002.fcs
Axes:
FSC-A
FSC-H
FSC-W
SSC-A
SSC-H
SSC-W
B_530-30-A
Time
Once loaded the parameters of the FCS file are available as properties.
julia> flowrun.last_modified
"2019-Oct-03 15:35:15"
julia> flowrun.p1n
"FSC-A"
There are many ways to index into the FCS file. You can index the FCS file as a matrix (actually an AxisArray
).
julia> flowrun[:, 1]
1-dimensional AxisArray{Float32,1,...} with axes:
:param, ["FSC-A", "FSC-H", "SSC-A", "SSC-H", "B1-A", "B1-H", "B2-A", "B2-H", "HDR-CE", "HDR-SE" … "V2-A", "V2-H", "Y1-A", "Y1-H", "Y2-A", "Y2-H", "Y3-A", "Y3-H", "Y4-A", "Y4-H"]
And data, a 23-element Vector{Float32}:
19.319384
12.838199
44.391308
20.214031
0.01834727
0.72980446
-0.25282443
0.4430968
â‹®
0.54869235
-0.027989198
0.48970717
4.498265
5.900927
0.02512901
0.3956769
This retrieves the values of all the parameters for the first event in the FCS file.
Similarly you can get the values of a single parameter for all events.
julia> flowrun[1, :]
1-dimensional AxisArray{Float32,1,...} with axes:
:event, 1:83562
And data, a 83562-element Vector{Float32}:
19.319384
22.961153
36.157864
30.91769
5.644829
14.188097
34.42944
4.4080987
â‹®
23.391977
-4.813841
-1.2413055
11.075016
13.712906
23.54529
5.740017
You can also take ranges of events.
julia> flowrun[1, end-99:end]
1-dimensional AxisArray{Float32,1,...} with axes:
:event, 83463:83562
And data, a 100-element Vector{Float32}:
4.576562
2.553804
10.608879
-6.4025674
-18.626959
6.1649327
24.049818
21.735662
â‹®
23.391977
-4.813841
-1.2413055
11.075016
13.712906
23.54529
5.740017
If you know the name of a parameter you can use that name to index.
julia> flowrun["FSC-A"]
1-dimensional AxisArray{Float32,1,...} with axes:
:event, 1:83562
And data, a 83562-element Vector{Float32}:
19.319384
22.961153
36.157864
30.91769
5.644829
14.188097
34.42944
4.4080987
â‹®
23.391977
-4.813841
-1.2413055
11.075016
13.712906
23.54529
5.740017
Or you can get multiple parameters at the same time.
julia> flowrun[["FSC-A", "FSC-H"]]
2-dimensional AxisArray{Float32,2,...} with axes:
:param, ["FSC-A", "FSC-H"]
:event, 1:83562
And data, a 2×83562 Matrix{Float32}:
19.3194 22.9612 36.1579 30.9177 … 11.075 13.7129 23.5453 5.74002
12.8382 3.40729 17.4995 14.0875 8.80171 5.29686 13.0893 11.3576
In general, any indexing that works with AxisArray
s should work the same with FCS files.
Here is an example which constructs a 2D histogram visualisation of a FCS file.
julia> using Gadfly
julia> p = plot(x=flowrun["FSC-A"], y=flowrun["SSC-A"], Geom.histogram2d,
Guide.xlabel("FSC-A"), Guide.ylabel("SSC-A"), Coord.cartesian(xmin=0, ymin=0))
julia> draw(PNG("example.png", 10cm, 7cm, dpi=300), p)