compare_flow_cytometry_populations
Read-only
One channel of an FCS file between two populations of the run (FlowJo's and FCS Express's population comparison): Welch's two-sample t-test, the Wilcoxon rank-sum test, the two-sample Kolmogorov–Smirnov test and Pearson's χ² on the two histograms over shared equal-width bins, each R's test on the populations' linear values.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| A | No | additional negative decades. Only applies when scale is logicle or hyperlog or flowcore-logicle or fasinh. | |
| M | No | decades of the full scale. Only applies when scale is logicle or hyperlog or flowcore-logicle or fasinh. | |
| T | No | top of scale; empty means the file's largest fluorescence $PnR. | |
| W | No | linear width in decades. Only applies when scale is logicle or hyperlog or flowcore-logicle. | |
| scale | No | the display scale of the fluorescence channels (scatter and time stay linear): used for the plot, the threshold and, with `stats_on: scaled`, the statistics. Values: logicle (Logicle (Gating-ML 2.0, Moore & Parks)), fasinh (ArcSinh (Gating-ML 2.0 fasinh)), arcsinh (ArcSinh with a cofactor (asinh(x / c), Cytobank and CyTOF)), hyperlog (Hyperlog (Gating-ML 2.0, Bagwell)), flowcore-logicle (Logicle on a 0–M axis (flowCore)), wsp-biex (Biex (FlowJo 10, channels 0–4096)), flin (Linear (Gating-ML flin)). | logicle |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| gating | No | a Gating-ML 2.0 document in the project, by name or id; empty for no gating (every statistic is then of all events). | |
| plot_x | No | channel (PnN or PnS) on the density plot's x axis; empty for no plot. | |
| plot_y | No | channel on the plot's y axis. | |
| derived | No | derived parameters, `name = expression` separated by `;` (FlowJo's vocabulary: channels by name or [name], + − * / % ^, abs ceil floor neg round max min pow exp ln log sqrt and the trig functions); each becomes a channel of the run. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| cofactor | No | the c in asinh(x / c): 5 is the CyTOF convention, 150 a common one for fluorescence. Only applies when scale is arcsinh. | |
| document | No | the FCS file, by name or id; may be left empty when the project holds exactly one. | |
| biex_width | No | FlowJo biex width basis (negative; FlowJo's default -10). Only applies when scale is wsp-biex. | |
| compare_bins | No | equal-width histogram bins over both populations’ range, for the χ² test. | |
| compensation | No | `auto`: the file's own $SPILLOVER/$SPILL when it has one, else none; `file`: that, refusing a file without one; `none`: leave the values as acquired. Values: auto (automatic), file (file's own matrix), none (none). | auto |
| population_a | No | population A; empty for all events. | |
| population_b | No | population B; empty for all events. | |
| biex_negative | No | FlowJo biex extra negative decades. Only applies when scale is wsp-biex. | |
| compare_channel | No | the channel compared (PnN, PnS or a derived name); empty for the first fluorescence channel. | |
| plot_population | No | the population plotted; empty for all events. | |
| compensation_method | No | which published algorithm: FlowKit's solve(Sᵀ, Xᵀ) or flowCore's X · S⁻¹. They agree to ~1e-15 of full scale. Values: flowkit (solve(Sᵀ, Xᵀ) (FlowKit)), flowcore (X · S⁻¹ (flowCore)). Only applies when compensation is auto or file. | flowkit |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| ks_d | Yes | Kolmogorov–Smirnov D | |
| tests | Yes | every test: method, statistic, parameter, p-value; the χ² histograms | |
| welch_p | Yes | Welch's t-test p-value | |
| rank_sum_p | Yes | Wilcoxon rank-sum p-value |