v0.7.5 — a hierarchy you can write by hand: import and save gates and populations as CSV

A hierarchy you can write by hand

The barcode-scheme file has become a general hierarchy file, and the buttons are now Import hierarchy CSV and Save hierarchy CSV. A population is one line, # population: B cells < Live = CD19+, not CD3+: the name, the parent after <, and the gates, with not for a NOT-reference. Leave the parent out and the population nests under the previous line. A gate is one line, # gate: CD3+ | rectangle | CD3 x SSC-A | asinh, linear | x 2..8 | y 0..200000: name, rectangle or polygon, the two channels joined by x, the scale, then the shape as ranges or as (x,y) points. A file of such lines imports as a tree under the population you choose, or into a new hierarchy. Mistakes are reported with their line number rather than guessed at, and a file that Excel has quoted still reads.

For a CyTOF debarcoding scheme the same lines sit above the sample table and describe the QC populations, so the whole strategy is in one file. A gate named without a # gate: line of its own takes its shape from the template, which keeps a hand-written file short: two population lines naming the standard gates are enough. A gate used by two populations is created once and shared, and gates the workspace already has are reused by name and channels.

Saving writes any workspace the same way: every polygon and rectangle gate and every population naming its parent, plus, for a debarcoding strategy, the sample table and the template. Quadrant and ellipse gates cannot be written in this form and are listed at the top of the file. A saved file rebuilds the same gates and populations when imported, with no template needed.