It extracts events matrices and appends the pData to it so that ggplot can use the pData for facetting.

# S3 method for flowFrame
fortify(model, data, ...)

# S3 method for flowSet
fortify(model, data, ...)

# S3 method for ncdfFlowList
fortify(model, ...)

# S3 method for GatingSetList
fortify(model, ...)

# S3 method for GatingSet
fortify(model, ...)

Arguments

model

flowFrame, flowSet or GatingSet

data

not used.

...

not used.

Value

data.table

data.table

data.table

Examples

dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) attr(gs, "subset") <- "CD4" #must attach subset information to GatingSet object before foritfying it fortify(gs)
#> .rownames name FSC-A FSC-H #> 1: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 140733.05 133376 #> 2: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 134347.02 125651 #> 3: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 101553.95 96602 #> 4: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 87721.18 79682 #> 5: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 112648.49 106622 #> --- #> 34028: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 91501.85 86287 #> 34029: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 104606.81 97939 #> 34030: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 117452.62 111203 #> 34031: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 104229.41 100303 #> 34032: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 110641.73 106703 #> FSC-W SSC-A <B710-A> <R660-A> <R780-A> <V450-A> <V545-A> #> 1: 69150.98 91113.96 3106.004 3302.719 2073.3540 2996.536 1795.1975 #> 2: 70071.60 70116.48 3128.845 1834.073 1607.8027 2507.708 1727.7843 #> 3: 68895.48 44620.80 2902.931 2458.440 482.8756 2700.848 1561.6256 #> 4: 72147.98 66181.08 2928.725 1382.240 1510.5111 2500.461 1501.8810 #> 5: 69240.23 49759.08 2832.599 1277.941 714.8516 2482.187 517.0981 #> --- #> 34028: 69496.75 68497.80 2984.366 2149.552 334.4934 2733.177 1588.8068 #> 34029: 69997.77 40012.56 2821.356 2043.574 1554.6113 2629.725 1590.2513 #> 34030: 69219.13 42007.56 3104.546 2757.161 782.6583 2763.769 1641.5566 #> 34031: 68101.44 40349.40 2920.189 2309.451 1579.1660 2657.493 1711.2170 #> 34032: 67955.13 39222.12 2959.566 2247.059 364.4596 2603.507 1021.9473 #> <G560-A> <G780-A> Time #> 1: 2397.642 2860.906 0.002 #> 2: 2194.188 1001.111 0.007 #> 3: 2759.033 3263.364 0.015 #> 4: 2223.328 1044.804 0.020 #> 5: 2173.669 1665.517 0.021 #> --- #> 34028: 2481.661 2454.105 295.269 #> 34029: 2342.940 2705.288 295.275 #> 34030: 2504.883 2348.783 295.317 #> 34031: 2271.206 1825.845 295.329 #> 34032: 2160.773 2825.193 295.380
fs <- gs_pop_get_data(gs, "CD8") fortify(fs)#fs is a flowSet/ncdfFlowSet
#> .rownames name FSC-A FSC-H #> 1: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 127717.88 119616 #> 2: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 84330.34 77826 #> 3: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 113783.64 107160 #> 4: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 103148.27 97894 #> 5: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 110324.17 106074 #> --- #> 14560: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 102727.06 94475 #> 14561: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 83445.57 75251 #> 14562: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 100791.84 94089 #> 14563: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 130091.12 122710 #> 14564: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 95898.64 88870 #> FSC-W SSC-A <B710-A> <R660-A> <R780-A> <V450-A> <V545-A> <G560-A> #> 1: 69974.92 76954.91 1296.8107 1931.995 3769.838 2749.284 1660.914 2883.802 #> 2: 71013.20 66052.55 1465.2563 1523.407 3702.229 2657.550 1612.924 2800.220 #> 3: 69586.83 62380.92 702.0428 1987.221 3515.332 2662.169 1504.550 2636.746 #> 4: 69053.52 47501.16 1390.0245 1483.048 3615.137 2466.290 1489.376 1574.406 #> 5: 68161.90 34369.44 873.0049 2161.021 3541.025 2420.300 1641.068 2183.459 #> --- #> 14560: 71260.34 65382.24 1230.4995 1108.483 3658.750 2514.224 1823.440 1003.388 #> 14561: 72672.64 87513.72 803.3681 1025.842 3718.617 2378.552 1611.274 1642.994 #> 14562: 70204.73 76909.55 1565.2583 2149.152 3852.465 2640.989 1611.140 2159.423 #> 14563: 69478.05 44694.72 1382.2026 1212.209 3426.707 2435.800 1783.091 1653.393 #> 14564: 70719.18 58815.12 864.5154 1592.644 3717.394 2332.334 1551.008 1315.681 #> <G780-A> Time #> 1: 3480.662 0.00700000 #> 2: 3415.069 0.01500000 #> 3: 2711.044 0.04800000 #> 4: 2576.902 0.06699999 #> 5: 3235.186 0.06800000 #> --- #> 14560: 3320.624 295.16098022 #> 14561: 1203.638 295.27697754 #> 14562: 3430.178 295.28399658 #> 14563: 1511.588 295.29098511 #> 14564: 2399.039 295.30499268
fr <- fs[[1]] fortify(fr)#fr is a flowFrame
#> .rownames name FSC-A FSC-H #> 1: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 127717.88 119616 #> 2: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 84330.34 77826 #> 3: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 113783.64 107160 #> 4: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 103148.27 97894 #> 5: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 110324.17 106074 #> --- #> 14560: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 102727.06 94475 #> 14561: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 83445.57 75251 #> 14562: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 100791.84 94089 #> 14563: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 130091.12 122710 #> 14564: CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs 95898.64 88870 #> FSC-W SSC-A <B710-A> <R660-A> <R780-A> <V450-A> <V545-A> <G560-A> #> 1: 69974.92 76954.91 1296.8107 1931.995 3769.838 2749.284 1660.914 2883.802 #> 2: 71013.20 66052.55 1465.2563 1523.407 3702.229 2657.550 1612.924 2800.220 #> 3: 69586.83 62380.92 702.0428 1987.221 3515.332 2662.169 1504.550 2636.746 #> 4: 69053.52 47501.16 1390.0245 1483.048 3615.137 2466.290 1489.376 1574.406 #> 5: 68161.90 34369.44 873.0049 2161.021 3541.025 2420.300 1641.068 2183.459 #> --- #> 14560: 71260.34 65382.24 1230.4995 1108.483 3658.750 2514.224 1823.440 1003.388 #> 14561: 72672.64 87513.72 803.3681 1025.842 3718.617 2378.552 1611.274 1642.994 #> 14562: 70204.73 76909.55 1565.2583 2149.152 3852.465 2640.989 1611.140 2159.423 #> 14563: 69478.05 44694.72 1382.2026 1212.209 3426.707 2435.800 1783.091 1653.393 #> 14564: 70719.18 58815.12 864.5154 1592.644 3717.394 2332.334 1551.008 1315.681 #> <G780-A> Time #> 1: 3480.662 0.00700000 #> 2: 3415.069 0.01500000 #> 3: 2711.044 0.04800000 #> 4: 2576.902 0.06699999 #> 5: 3235.186 0.06800000 #> --- #> 14560: 3320.624 295.16098022 #> 14561: 1203.638 295.27697754 #> 14562: 3430.178 295.28399658 #> 14563: 1511.588 295.29098511 #> 14564: 2399.039 295.30499268