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OpenReadout

table

table returns rows of a table: FCS events, plate-reader values, spike, event or peak tables. For FCS files it can compensate and transform the values and add population membership from a FlowJo workspace or Gating-ML file.

openreadout table [OPTIONS] [FILE]...

info lists a file’s tables under tables[].

Flags

  • --json: print the JSON wrapper instead of text.
  • --table N: table index (FCS data set, plate read). Default 0 (in a batch table, every table).
  • --first-row N: zero-based first row. Default 0.
  • --max-rows N: rows to return, at most 1000000. Default 100.
  • --filter CONDITION: only rows meeting COLUMN OP NUMBER, with OP one of >, >=, <, <=, ==, !=. Repeatable or joined with &&. The whole table is scanned.
  • --count: count the matching rows only; return no rows.

Flow cytometry

  • --compensate [auto|fcs|gating]: compensate first. Without a value, auto: the gating file’s matrix when one is given, else the file’s own spillover matrix.
  • --transform SPEC: transform after compensation: logicle, arcsinh, hyperlog, log, linear, biex, flowjo-log, arcsinh-cofactor, with parameters as NAME:K=V,… (for example logicle:T=262144,W=0.5,M=4.5,A=0), or workspace for the FlowJo sample’s own transforms.
  • --parameter NAME: parameters to transform. Default: every fluorescence parameter. Repeatable or comma-separated.
  • --workspace WSP: FlowJo workspace (.wsp).
  • --gatingml XML: Gating-ML 2.0 document.
  • --sample NAME: workspace sample, by name or id.
  • --population PATH: append a 0/1 column gate:<PATH> with this population’s membership. Repeatable.

Without these flags, table returns raw stored values.

Several files, a directory or a glob give one summary table: per FCS file and parameter (events, median, mean, sd, min, max), or per plate well and read. table takes the flags in Several inputs and the batch table flags.

Examples

Terminal window
$ openreadout table doctor.fcs --max-rows 3
FSC-A  SSC-A  Time
0.5  1.5  2.5
10.5  11.5  12.5
20.5  21.5  22.5
# rows 0..3 of 10 (table 0)

Count events without exporting them:

Terminal window
$ openreadout table doctor.fcs --filter "FSC-A > 50" --count
# 5 of 10 rows (50.0000%) meet FSC-A > 50

Compensated, logicle-transformed events with membership of one gate:

Terminal window
openreadout table sample.fcs --compensate --transform logicle \
  --workspace analysis.wsp --population /Lymphocytes/Singlets --json

To count every population of a gating tree, use analyze gate.

JSON

table, batch table.

Run openreadout table --help for the full help of your installed version.