GateLabR 1.6.5

GateLabR 1.6.5

Embedded core

• GateLab 0.11.0 (GateLab-dev 41448da6), up from 0.10.1. The Plotting tab draws a channel per cell as violins, boxes, split violins or ridgelines and a channel statistic per sample as boxes, bars or points, with Kruskal-Wallis, pairwise Wilcoxon (Holm) and signed-rank tests, several named charts saved with the workspace, shelves for rows, columns and pages, and the table behind a chart. Layout is a page editor: copy and paste between sheets, panel letters, shapes, formatted text, rulers and guides, placed images and a written legend; the legend of a chart block is a key, and its frame holds the chart at the text sizes of the sheet. Illustration overlays chosen populations and puts chart panels in the figure grid. A population has one colour in every tab, set in the population tree, and the workspace one figure style. New Workspace and Open Workspace ask before unsaved changes are replaced.
• The file reading, writing and gate evaluation of the core carry 76 corrections from an audit, each with a regression test. Among them: a workspace holding strategy, derived-channel or image settings can be reopened; a file with no $TOT opens; control characters are left out of written Gating-ML names; a GatingSet or Cytobank-model population that excludes a population of another branch is left out by name, where it was imported with the wrong events; a Gating-ML rectangle with min above max is empty, and a population cycle refuses the file. Gate evaluation is otherwise unchanged.
• Gating-ML export keeps representable empty quadrant regions and their dependent populations. Changing the transform of one channel keeps the chosen range of the other. Illustration and Layout keep unrelated gate outlines out of an empty branch. Plotting tables use sample headings in R without renaming user metadata columns.

R package

• gatelabSync() refuses an object whose cells are not those of the app, sample by sample and in order. It compared the cell count and the column names only, and CATALYST::prepData() builds an object without column names, so an object whose events were reordered within a sample passed, and the next Save to SCE or colData write placed the values of each sample on other cells. Without unique column names the order is proven by the event ids of the last save, or by an assay both objects hold being equal on the channels both hold.
• The package logo and the header of the embedded app use the blue GateLabR branding and the wordmark alone.

Compatibility

• GateLabR 1.6.4 refuses a workspace saved into an object by 1.6.5, with a message, when it is saved with a compensation profile and also holds named charts or an edited figure style. Other workspaces open in both.

Tested

• testthat: 333 tests, 2,809 expectations, 0 failed. R CMD check: 0 errors, 0 warnings, 3 notes (installed size, future timestamps, assignments to the global environment).
• Host parity check on the served package: 23 of 23.