GateLabR 1.4.6

Save to SCE now stores which events every population holds, for every hierarchy, beside the workspace in metadata(sce)$gatelab_workspace$memberships, as one packed bitset per population. Four functions read it back without re-gating in R: gatelabHierarchies(), gatelabHierarchy() (one row per population with parent, depth, path, gates and count), gatelabPopulations() (a logical events-by-populations matrix) and gatelabLeafPopulation() (each event's deepest population as a factor, or "ungated"). The memberships remember the workspace revision they were computed at; after an autosave has moved the workspace on they are refused until the next explicit save, unless allow_stale = TRUE. Reading them on a subset SCE is refused, since the masks assume the original event order. If an explicit save reaches R without memberships, the accessors say the core that served it predates them, and the app's save message says when the R side stored none.

"Colour by" now offers the SCE's categorical colData columns: any factor, character or logical column with at most 254 levels, such as a FlowSOM or CATALYST merge level, so cluster composition can be watched while a gate is drawn. The dataset payload carries only the column names and level counts; a column's values are fetched when it is chosen, once, in the per-sample coded form the categorical export already uses. A named colour vector in metadata(sce)$gatelab_palettes[[column]] fixes the colours so the app matches the analysis figures.

Running from a clone with source("launch.R") now sources every file under R/, so functions added in new files are defined the same way as in the installed package.

The embedded GateLab core is GateLab-dev master at 7883c8a: on top of 0.7.5 it sends the memberships with an explicit save, colours by a hosted colData column, and, when the plot pools several checked files, labels gate counts pooled over the same files.