Applies a cs_signal_policy to the intensity measurements in a
cellspec object. A preferred finite value is used when its declared domain
accepts it; otherwise the configured fallback is tested using its own domain.
Default domains require values at least min_value. The "finite" domain
accepts negative finite values. Non-finite values remain unavailable in both.
Arguments
- x
A
cellspecobject.- policy
A
cs_signal_policycreated bycs_signal_policy().- image_id
Optional image identifier. When supplied, only cells from that image are returned.
Value
A list with signal, a cells by markers numeric matrix, source, a
character matrix describing the selected source, and policy, the
validated policy. Source values are "<compartment>:<statistic>",
"fallback:<compartment>:<statistic>" or "unavailable".
Examples
x <- cs_example()
policy <- cs_signal_policy(cs_markers(x))
selected <- cs_signal_matrix(x, policy)
selected$signal[, 1:2]
#> DAPI CD3e
#> 1 31.7296 16.6653
#> 2 5.5744 164.4467
#> 3 18.3195 33.5342
#> 4 19.2818 190.3371
#> 5 29.6346 6.4369
#> 6 24.0813 26.5155
#> 7 133.7387 48.3400
#> 8 108.9936 205.9034
#> 9 41.1782 29.0966
#> 10 13.9255 22.0039
#> 11 5.2126 76.4789
#> 12 31.0010 20.5449
#> 13 171.0040 159.6717
#> 14 107.9310 85.1976
#> 15 21.0609 48.9259
#> 16 101.9609 61.6761
#> 17 13.1304 39.8273
#> 18 114.0909 15.1845
#> 19 95.1428 18.5123
#> 20 41.6574 113.3236
#> 21 166.2902 27.1171
#> 22 5.5461 29.0827
#> 23 212.9764 136.4018
#> 24 6.2627 19.3159
#> 25 41.3807 39.1086
#> 26 55.8962 1.3282
#> 27 7.9960 12.4137
#> 28 17.9735 67.3726
#> 29 15.4342 6.7498
#> 30 14.3834 11.9688
#> 31 11.5762 38.0856
#> 32 120.4570 14.4792
#> 33 21.5935 11.4580
#> 34 147.1378 14.7547
#> 35 10.1984 23.4833
#> 36 8.6335 29.6572
#> 37 13.1495 5.8615
#> 38 11.8506 8.1795
#> 39 15.5081 11.5671
#> 40 47.0861 44.2072
#> 1 75.9318 136.2283
#> 2 119.9755 130.8204
#> 3 5.0617 8.5446
#> 4 1.8171 41.4087
#> 5 77.7874 217.8956
#> 6 26.8731 5.8744
#> 7 21.4012 142.1992
#> 8 27.7239 14.3220
#> 9 4.8217 28.4807
#> 10 116.8894 17.2876
#> 11 24.3082 23.9871
#> 12 11.1367 23.6451
#> 13 7.5043 4.3126
#> 14 9.0503 29.2059
#> 15 11.8600 68.7578
#> 16 29.0260 11.1006
#> 17 12.5941 22.0476
#> 18 146.1850 178.8168
#> 19 12.4994 16.5780
#> 20 6.6639 73.5430
#> 21 49.6253 6.9933
#> 22 77.0584 10.3396
#> 23 8.5926 13.6475
#> 24 5.2848 141.8186
#> 25 22.6272 17.0960
#> 26 96.3507 29.3634
#> 27 16.4542 21.4546
#> 28 124.4366 10.0016
#> 29 18.8177 113.8623
#> 30 20.2170 9.8800
#> 31 85.1764 225.9706
#> 32 12.2432 208.1091
#> 33 35.6233 73.9157
#> 34 98.1132 81.6005
#> 35 13.6345 27.1717
#> 36 9.1107 110.1646
#> 37 16.6287 28.4719
#> 38 91.2071 13.3398
#> 39 29.7930 161.9798
#> 40 307.1858 85.0682