Do proper .fcs flow-cytometry files already have the gating hierarchy, so one may calculate cell-counts without extra work?
https://github.com/whitews/FlowKit/
# setup some file paths for our data
base_dir = "data/8_color_data_set"
sample_path = os.path.join(base_dir, "fcs_files")
wsp_path = os.path.join(base_dir, "8_color_ICS.wsp")
session = fk.Session(sample_path)
session.import_flowjo_workspace(wsp_path)
# that's it, let's see what sample groups were loaded
session.get_sample_groups()
['default', 'All Samples', 'DEN']
# I happen to know all the "real" analysis is within the "DEN" group
sample_group = 'DEN'
# and the sample that are included in the group
session.get_group_sample_ids(sample_group)
['101_DEN084Y5_15_E03_009_clean.fcs',
'101_DEN084Y5_15_E01_008_clean.fcs',
'101_DEN084Y5_15_E05_010_clean.fcs']
# so what is the gating hierarchy for this group
print(session.get_gate_hierarchy(sample_group))
root
╰── Time
╰── Singlets
╰── aAmine-
╰── CD3+
├── CD4+
│ ├── CD107a+
│ ├── IFNg+
│ ├── IL2+
│ ╰── TNFa+
╰── CD8+
├── CD107a+
├── IFNg+
├── IL2+
╰── TNFa+
# looks good, let's go ahead and analyze them (using verbose mode to see each gate as it's processed)
session.analyze_samples(sample_group, verbose=True)
#### Processing gates for 3 samples (multiprocessing is enabled - 3 cpus) ####
101_DEN084Y5_15_E03_009_clean.fcs: processing gate Time
101_DEN084Y5_15_E03_009_clean.fcs: processing gate Singlets
101_DEN084Y5_15_E03_009_clean.fcs: processing gate aAmine-
101_DEN084Y5_15_E01_008_clean.fcs: processing gate Time
101_DEN084Y5_15_E01_008_clean.fcs: processing gate Singlets
101_DEN084Y5_15_E01_008_clean.fcs: processing gate aAmine-
101_DEN084Y5_15_E05_010_clean.fcs: processing gate Time
101_DEN084Y5_15_E03_009_clean.fcs: processing gate CD3+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate Singlets
101_DEN084Y5_15_E05_010_clean.fcs: processing gate aAmine-
101_DEN084Y5_15_E03_009_clean.fcs: processing gate CD4+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate CD3+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate CD4+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate CD3+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate CD8+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate CD4+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate CD8+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate CD107a+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate CD8+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate CD107a+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate IFNg+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate CD107a+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate IFNg+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate IL2+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate IFNg+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate IL2+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate TNFa+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate IL2+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate TNFa+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate CD107a+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate TNFa+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate CD107a+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate IFNg+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate CD107a+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate IFNg+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate IL2+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate IFNg+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate IL2+
101_DEN084Y5_15_E03_009_clean.fcs: processing gate TNFa+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate IL2+
101_DEN084Y5_15_E01_008_clean.fcs: processing gate TNFa+
101_DEN084Y5_15_E05_010_clean.fcs: processing gate TNFa+
# and a look a the results
session.get_group_report(sample_group)
sample gate_path gate_name gate_type quadrant_parent parent count absolute_percent relative_percent level
0 101_DEN084Y5_15_E03_009_clean.fcs (root,) Time RectangleGate None None 283968 99.999648 99.999648 1
1 101_DEN084Y5_15_E03_009_clean.fcs (root, Time) Singlets PolygonGate None Time 236780 83.382341 83.382635 2
2 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets) aAmine- PolygonGate None Singlets 161823 56.986150 68.343188 3
3 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-) CD3+ PolygonGate None aAmine- 132200 46.554377 81.694197 4
4 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+) CD4+ PolygonGate None CD3+ 81855 28.825330 61.917549 5
5 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+) CD8+ PolygonGate None CD3+ 46965 16.538777 35.525719 5
6 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) CD107a+ RectangleGate None CD4+ 59 0.020777 0.072079 6
10 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) CD107a+ RectangleGate None CD8+ 814 0.286651 1.733206 6
7 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) IFNg+ RectangleGate None CD4+ 598 0.210586 0.730560 6
11 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) IFNg+ RectangleGate None CD8+ 1224 0.431033 2.606196 6
8 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) IL2+ RectangleGate None CD4+ 64 0.022538 0.078187 6
12 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) IL2+ RectangleGate None CD8+ 127 0.044723 0.270414 6
9 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) TNFa+ RectangleGate None CD4+ 288 0.101420 0.351842 6
13 101_DEN084Y5_15_E03_009_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) TNFa+ RectangleGate None CD8+ 821 0.289116 1.748110 6
0 101_DEN084Y5_15_E01_008_clean.fcs (root,) Time RectangleGate None None 290166 99.997932 99.997932 1
1 101_DEN084Y5_15_E01_008_clean.fcs (root, Time) Singlets PolygonGate None Time 239001 82.365287 82.366990 2
2 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets) aAmine- PolygonGate None Singlets 164655 56.743931 68.893017 3
3 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-) CD3+ PolygonGate None aAmine- 133670 46.065782 81.181865 4
4 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+) CD4+ PolygonGate None CD3+ 82484 28.425899 61.707189 5
5 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+) CD8+ PolygonGate None CD3+ 47165 16.254153 35.284656 5
6 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) CD107a+ RectangleGate None CD4+ 68 0.023434 0.082440 6
10 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) CD107a+ RectangleGate None CD8+ 73 0.025157 0.154776 6
7 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) IFNg+ RectangleGate None CD4+ 4 0.001378 0.004849 6
11 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) IFNg+ RectangleGate None CD8+ 2 0.000689 0.004240 6
8 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) IL2+ RectangleGate None CD4+ 6 0.002068 0.007274 6
12 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) IL2+ RectangleGate None CD8+ 10 0.003446 0.021202 6
9 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) TNFa+ RectangleGate None CD4+ 21 0.007237 0.025459 6
13 101_DEN084Y5_15_E01_008_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) TNFa+ RectangleGate None CD8+ 8 0.002757 0.016962 6
0 101_DEN084Y5_15_E05_010_clean.fcs (root,) Time RectangleGate None None 284846 99.844369 99.844369 1
1 101_DEN084Y5_15_E05_010_clean.fcs (root, Time) Singlets PolygonGate None Time 235331 82.488345 82.616923 2
2 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets) aAmine- PolygonGate None Singlets 160955 56.418031 68.395154 3
3 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-) CD3+ PolygonGate None aAmine- 131305 46.025097 81.578702 4
4 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+) CD4+ PolygonGate None CD3+ 81135 28.439483 61.791249 5
5 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+) CD8+ PolygonGate None CD3+ 46546 16.315328 35.448764 5
6 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) CD107a+ RectangleGate None CD4+ 70 0.024536 0.086276 6
10 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) CD107a+ RectangleGate None CD8+ 306 0.107259 0.657414 6
7 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) IFNg+ RectangleGate None CD4+ 9 0.003155 0.011093 6
11 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) IFNg+ RectangleGate None CD8+ 348 0.121981 0.747647 6
8 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) IL2+ RectangleGate None CD4+ 8 0.002804 0.009860 6
12 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) IL2+ RectangleGate None CD8+ 65 0.022784 0.139647 6
9 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD4+) TNFa+ RectangleGate None CD4+ 28 0.009815 0.034510 6
13 101_DEN084Y5_15_E05_010_clean.fcs (root, Time, Singlets, aAmine-, CD3+, CD8+) TNFa+ RectangleGate None CD8+ 336 0.117775 0.721867 6
