NEWS
MultiAssaySpatialExperiment 0.99.12
Documentation
- Replaced
\dontrun{} with \donttest{} in the four platform-reader
examples that need real vendor output (readHDF5ForMASE(),
readVisiumMASE(), readVisiumHDMASE(), readXeniumMASE()), per
BiocCheck: \dontrun{} examples never run, even under
R CMD check --run-donttest or interactive example(), while
\donttest{} ones do, which is what lets Bioconductor's periodic checks
catch these examples rotting out from under a real file-format change.
Verified directly with BiocCheck: no ERROR or WARNING, and its
dontrun/donttest usage NOTE now reports only \donttest{} tags.
MultiAssaySpatialExperiment 0.99.11
Documentation
- A fresh review of the current vignettes against the standards the
Bioconductor review has consistently applied (prose over bullets, runnable
code over listings, consistent heading conventions) found four residual
issues, all fixed:
- The introduction vignette's own "Next steps" section was never actually
renamed to "See also", unlike its two siblings: it still read
# Where to go next, in a full-sentence bullet style that didn't match
the "Title: short phrase" convention -workflows.Rmd and
-usecases.Rmd already use consistently. Brought into line.
- Working with MultiAssaySpatialExperiment's "Validation checklist"
section listed construction invariants but never demonstrated any of
them, the same "listing instead of demonstrating" pattern already fixed
elsewhere in that vignette. Added two runnable, verified examples: a
sampleMap mismatch that is silently dropped with a message during
harmonization, and a broken spatialMap that fails validObject()
outright, since a dangling geometry reference cannot be silently
dropped the way a sampleMap row can.
- Converted six narrative/comparison bulleted lists in
-usecases.Rmd and
-workflows.Rmd to prose (transcript use cases, two Xenium/Visium
background comparisons, a data-preparation listing, the aggregation
strategy rationale, and the rasterization/vectorization preview).
Structural lists (vendor output file listings, parameter tables, the
numbered platform-integration rationale, "See also") were left alone;
those are legitimate uses of a list, not the pattern being fixed.
- The entity-relationship diagram's
experiments(mase) box had no visible
connection to the ExperimentList class named in the surrounding prose;
relabeled to experiments(mase) (ExperimentList), matching the
Experiment (SummarizedExperiment) convention the same diagram already
uses for a different entity.
- While regenerating the diagram above, found that
build_diagrams.sh
itself would silently regenerate it at 784x527, the exact low resolution
from a previous round of review, since the script never recorded the
scale factor actually used to produce the checked-in 3168x2128 image, and
its default background (transparent) rendered incorrectly in at least
one viewer. Both fixed (-s 4, default background changed to white);
the diagram is now reproducible from the script as checked in.
MultiAssaySpatialExperiment 0.99.10
Documentation
- Fixed the
R CMD check "Rd cross-references" NOTE: 34 roxygen \linkS4class{}
references to classes defined in other packages (DataFrame and List/
SimpleList in S4Vectors; SpatialExperiment; SingleCellExperiment;
MultiAssayExperiment and ExperimentList in MultiAssayExperiment;
SummarizedExperiment) had no package anchor, across 7 source files and
the 12 man pages they generate. \linkS4class{X} only resolves without a
warning for classes in the current package; cross-package references now
use \link[pkg:X-class]{X}. Classes defined in this package itself
(MultiAssaySpatialExperiment, RasterLayerList, PointsLayerList,
ShapesLayerList, SpatialLayerList) were left as plain \linkS4class{},
since those never needed anchoring.
- Fixed the stale
http:// Bioconductor badge URL in README.md (R CMD check flagged it as a 301 redirect to https://).
Bug fixes
- Added the missing
Matrix Suggests dependency, used directly in
tests/ but not declared, which R CMD check flagged as an unstated
test dependency.
MultiAssaySpatialExperiment 0.99.9
Documentation
- Fixed a real terminology collision the 0.99.7 copy edit missed: three
vignettes built a shapes layer literally named
"regions", which collides
with spatialMap's own region column (the points/shapes layer name each
row references). Renamed to cells in the introduction vignette and
anatomical_regions in use cases (where the layer is tissue-scale, not
per-cell); added a paragraph after annotateWithRegions() in the
introduction distinguishing the pre-existing region column from the new
annotation column the function adds. A colData column separately named
region in Working with MultiAssaySpatialExperiment's subsetting example
collided for an unrelated reason and is now zone. The cheatsheet's
annotateWithRegions() entry made the identical mistake in prose
("records the region on spatialMap") and now describes what the function
actually does: add a new column named for the shapes layer.
- Introduced
ExperimentList, colData and sampleMap before their first
use in the introduction vignette instead of leaving them to appear
unexplained in code output, added the "each row reads ..." sentence for
sampleMap that Design of MultiAssaySpatialExperiment already used for
spatialMap, explained st_polygon()/st_sfc()/sfc_POLYGON where they
are first used, and noted that read*() functions exist for real platform
data before walking through manual construction.
- Copy edit across all five vignettes for correctness, consistency, clarity
and concision. Correctness: a cross-reference in use cases promised
"coercion details and limitations" in a section that does not discuss
them (removed); a heading and a summary bullet called a direct
point-in-polygon count "the deconvolution result"/"cell type
deconvolution" when the adjacent body text explicitly says it is not
deconvolution (reworded to "composition result"/"cell type transfer");
the use cases summary referenced a "deliberately plain R" sentence that
had been removed from Workflow 2 earlier in this same round of edits
(reworded to stand on its own); "FOV" was used before being spelled out;
a comma splice in the
subsetByAssay() note in Working with
MultiAssaySpatialExperiment. Consistency: "Part 1: Data Import" and
"Part 2: Real-World Workflows" used Title Case where every other heading
in the same document uses sentence case after a colon; the Xenium reader
section had an "Options" table that the Visium, CosMx and MERSCOPE
sections did not (added, values taken from each function's own roxygen
@param docs); two sentences in use cases used first-person-plural
narrative voice ("We will create...") where the rest of the document
describes what the code does. Concision: the entity-relationship diagram's
intro sentence in Design of MultiAssaySpatialExperiment duplicated its
own figure caption almost verbatim (trimmed); the "Scientific question"
callout in use cases used more promotional language ("leverage...
improve our understanding of") than the plain register used elsewhere in
the document.
Bug fixes
aggregateByRegion(x, by, FUN = "count") named its result column region
regardless of by; the "sum"/"mean" branches already name result
columns after by, so "count" was the odd one out and, for any by
other than a layer literally named "region", produced a column name that
did not match the argument that produced it. It now names the column after
by, e.g. by = "cells" produces a cells column.
Internal changes
- Replaced fourteen further
for loops with lapply()/vapply()/
Reduce()/vectorized code, in the same spirit as 0.99.8's refactor:
spatialMatch()'s two loops (one needed no loop or apply at all, just
vectorized arithmetic); .subsetSpatialMapByColumn() and
.subsetMASEBySpatialFilter(); .aggregateMatrixByRegion() and
aggregateByRegion()'s per-assay loop; .mergeLayerList() and
.reduceLayerList() (the latter was a manual fold, now a Reduce());
four loops in .check_visiumhd_files()/.build_mase_from_visiumhd(), two
of which re-tested a loop-invariant is.null(boundaries) condition on
every iteration and are now hoisted out; the ShapesLayerList()
constructor's coercion loop; the annotGeometryNames loop in the
SpatialFeatureExperiment coercion; .spatialImages_from_imgData()'s
rename-and-filter loop; and a test helper's loop around file.remove(),
which already vectorizes. Verified against the full test suite plus
targeted re-runs of every touched test file, and (for spatialMatch()'s
vectorized branch) a direct comparison against the original loop's output.
- Consolidated the fifteen file-pattern-search loops kept as-is in 0.99.8
(correctly: they
break on the first match, so an apply variant can't
short-circuit) into two shared helpers, .firstExistingPath() and
.firstMatchingFile(), in a new "File discovery" section of
MultiAssaySpatialExperiment-read-helpers.R. Those fifteen loops were the
same six-line block copy-pasted across the CosMx, MERSCOPE, Xenium and
Visium readers; all fifteen call sites now delegate to one of the two
helpers instead, including the one Xenium case that also checks
dir.exists() (passed in as a check override). Behavior is unchanged,
confirmed by directly unit-testing both helpers against no-match, match,
and the Xenium dual-check case, and by the full read-technology test file
(151 assertions) passing unchanged. for loops in R/ go from 43 to 15
overall between this entry and 0.99.8; the remainder are the validity-check
accumulators, side-effect-only loops, and upstream-fidelity ports (e.g.
.get_img_idx_mase()) that 0.99.8 already explains.
MultiAssaySpatialExperiment 0.99.8
Internal changes
subsetByBoundingBox() and subsetByPolygon() were structurally identical
apart from the functions used to index each layer, and each contained four
near-duplicate loops. Both now delegate to one .subsetMASEByGeometry()
engine, which also removes redundant work: each method previously indexed
every spatial layer twice, once to build the retained-instance map and
again, with identical arguments, to build the filtered layers, so
subsetByPolygon() ran its point-in-polygon join twice per layer on every
call. Equivalence was checked against the previous implementation across
partial-hit, everything-retained and empty-result cases for both methods,
comparing dimensions, layer contents, layer names and spatialMap.- The review asked whether the package's
for loops could use the apply
family. Eight are removed by the refactor above. Of the remainder, fifteen
are file-pattern searches that break on the first hit, where an apply
variant cannot short-circuit and would test every candidate path; the rest
either fold state across iterations or exist for their side effects, where a
loop is the clearer form. The two examples named in the review are kept:
.get_img_idx_mase() is a near-verbatim port of
SpatialExperiment:::.get_img_idx(), deliberately structured like its
upstream counterpart, and .import_SFE_generics() is a two-line side-effect
loop registering generics.
MultiAssaySpatialExperiment 0.99.7
Documentation
- Expanded the narrative in MultiAssaySpatialExperiment use cases, which the
Bioconductor review found short on explanation of what each step does and
why. The reader sections now describe the arguments that actually change the
result and what they cost; the coercion sections say why you would coerce
rather than re-read the vendor output, and what survives each conversion;
Workflow 3 states the problem it solves instead of listing what could be
done; Workflow 4 explains why its steps are in that order, since the point of
that section is the ordering; and the summary says plainly what the container
does not do, which is also why the affine-transformation example is
deliberately plain R.
- Removed three further blocks of explanatory comments from code chunks
(
# The conversion: twice and # The combined MASE has:), matching the ones
already removed in 0.99.7. No cat() call or comment block now stands in for
prose in any vignette.
- Copy edit across all five vignettes for correctness, consistency, clarity and
concision. Substantive fixes: three cross-references named a vignette
MultiAssaySpatialExperiment Use Cases when the title is lower case; one
sentence in the introduction said an assay column belongs to a "sample" two
lines after establishing that it belongs to a specimen, which is the exact
distinction that section teaches. Consistency fixes: vignette
cross-references were split between bold and italic and are now uniformly
italic, as elsewhere in the suite; the two "See also" lists disagreed on
heading, ordering and capitalisation and are now identical in form; two
Oxford commas were brought into line with the prevailing style. One 60-word
sentence was split.
- Restructured the vignettes in response to the Bioconductor review, which
observed that the introduction read like a developer vignette. The
introduction is now motivation followed by a single worked example carried
from construction through subsetting, annotation and aggregation to
coercion, matching the shape of
SingleCellExperiment's intro.Rmd. The
slot-by-slot anatomy, the mapping tables and the entity-relationship
diagram move to a new Design of MultiAssaySpatialExperiment vignette,
which is both the split SingleCellExperiment makes between intro and
devel and the <Package>-design convention already used by the sibling
packages in this suite.
- Added a MultiAssaySpatialExperiment cheatsheet vignette, a one-page API
reference modelled on
MultiAssayExperiment's. Two vignettes previously
pointed readers at a cheatsheet that did not exist.
- Vignette files follow the suite naming convention, so pkgdown links the
introduction as the package landing page:
Introduction.Rmd becomes MultiAssaySpatialExperiment.Rmd,
WorkingWithMASE.Rmd becomes MultiAssaySpatialExperiment-workflows.Rmd,
and UseCases.Rmd becomes MultiAssaySpatialExperiment-usecases.Rmd.
- The entity-relationship diagram is rebuilt at roughly four times the
resolution, with entities declared in the order the text introduces them and
genuine per-entity colouring. The prose had described "tan" and "blue" boxes,
but the source set a single colour and defined no per-entity styling, so no
such distinction was ever rendered.
spatialImages and spatialLabels are
included for the first time; their absence was part of why the diagram and
its description could not be reconciled. Crow's-foot notation is now
explained.
- Added a prerequisites section stating what background is assumed, and that
sf is required only for the shapes slot.
- Replaced the remaining bullet lists that stood in for explanation with
prose, removed the
cat() calls that printed static workflow text from code
chunks, gave the subsetting, spatial-operation and coercion sections
runnable examples, and renamed headings that merely repeated the sentence
below them.
- The subsetting examples use two assays and distinguish specimen identifiers
(
P1, P2) from observation identifiers (S1...S4). With one assay whose
column names matched its specimen names, subsetting by specimen and by assay
column produced identical output and the distinction was invisible.
- Fixed bullet lists that were not separated from the preceding line, which
pkgdown did not render as lists.
- Renamed "Next steps" sections to "See also", as they enumerate the other
vignettes rather than a progression.
Bug fixes
- Added
Spatial to biocViews.
.check_visium_files() no longer builds a message with paste0() inside
the condition signal; the subdirectory name is computed once and reused.
Internal changes
- Removed four unused internal functions:
.spatialLabels_from_rasters(),
.read_label_rasters(), set_block_size() and list_technologies().
- Fixed the indentation of
else continuations in .mergeMASE(), the cbind
method, and the SpatialFeatureExperiment coercion.
MultiAssaySpatialExperiment 0.99.6
Bug fixes
- Fixed a spurious
no definition for class "MultiAssaySpatialExperiment"
warning (one per setAs()/setMethod() call registered in
.register_SFE_coercion()/.register_SFE_methods(), ~20 total) emitted
whenever SpatialFeatureExperiment was already loaded before
MultiAssaySpatialExperiment (e.g. library(SpatialFeatureExperiment); library(MultiAssaySpatialExperiment)). Registration in that case runs
synchronously inside .onLoad, which always completes before this
package is attached to search(); .sfe_ext_env (added in 0.99.5 to
work around namespace sealing) was parented to globalenv(), so at
registration time it couldn't yet see "package:MultiAssaySpatialExperiment"
to validate the class in the method signature. .sfe_ext_env is now
parented to this package's own namespace instead, where the class is
always immediately reachable regardless of attachment timing. Harmless
(registration and dispatch both still worked correctly), but noisy.
MultiAssaySpatialExperiment 0.99.5
Bug fixes
as(spe/sfe, "MultiAssaySpatialExperiment") now store the assay as a plain
SingleCellExperiment and keep all spatial content (colGeometries,
annotGeometries, unit, col-margin spatialGraphs) in MASE's own
points/shapes/spatialMap/colPair() layers, instead of retaining the
full SpatialExperiment/SpatialFeatureExperiment object. Previously,
writeParquet() (BiocDuckDB) only ever read those MASE-native layers, so
anything living only in a nested SFE's colGeometries beyond the primary
centroids, annotGeometries, or spatialGraphs was silently dropped on
write even though it looked preserved in memory. as(mase, "SpatialExperiment"/"SpatialFeatureExperiment") and the SFE-delegating
methods (dimGeometry, annotGeometry, bbox, unit, splitByCol,
aggregate, findDebrisCells) now reconstruct a real SPE/SFE view from
those native layers on demand; spatialGraphs/spatialGraph/
spatialGraphNames read colPair() directly. localResults is not
carried over by this coercion (no MASE-native home for it yet); it now
errors with a message that says so instead of a misleading
"no SpatialFeatureExperiment assay" message.- Fixed a registration bug where the entire
SpatialFeatureExperiment
integration (all coercions and the dimGeometry/unit/bbox/etc.
delegating methods) would silently fail to register whenever anything
loaded MultiAssaySpatialExperiment before the user loaded
SpatialFeatureExperiment in the same session (for example, loading
BiocDuckDB first, since it imports this package) -- as(sfe, "MultiAssaySpatialExperiment") would then silently fall back to the
generic SpatialExperiment coercion with no error. The deferred
registration hook ran after this namespace was already sealed, and
setAs()/setMethod() need to create a new top-level binding the first
time a generic is used from a namespace; that's forbidden once a
namespace is sealed, and the resulting error was masked by an
overly-broad grepl("locked", ...) catch in the load hook. Registration
now targets a small dedicated, never-sealed environment instead of this
namespace, which works regardless of load order; the test suite's own
pkgload::load_all() workaround for this (helper-sfe-register.R) is no
longer needed and has been removed.
Documentation
- Added the missing
@aliases coerce,...-method entries for the
list/List -> RasterLayerList/PointsLayerList/ShapesLayerList
coercions in ?SpatialLayerList-class; these were implemented but
undocumented, which R CMD check flagged as missing documentation
entries.
MultiAssaySpatialExperiment 0.99.4
Documentation
- Replaced em dashes with commas or colons in the vignettes.
MultiAssaySpatialExperiment 0.99.3
Documentation
- Added
URL and BugReports fields to DESCRIPTION.
- Added a package-level man page (
?MultiAssaySpatialExperiment).
MultiAssaySpatialExperiment 0.99.2
Documentation
- Added
\value sections (roxygen @return) to the MultiAssaySpatialExperiment
class, combine, subset, and SpatialExperiment-coercion man pages, and to
SpatialLayerList-class, documenting the values returned by the constructors,
accessors, replacement, coercion, combining, and subsetting methods. Resolves
the R CMD BiocCheck "missing \value" WARNING.
MultiAssaySpatialExperiment 0.99.1
Bug fixes
readMERSCOPEMASE() and readCosMxMASE() now have runnable examples backed
by minimal mock output directories bundled under inst/extdata/
(merscope_mock/, cosmx_mock/; generated by inst/scripts/make-example-mocks.R).
This raises the share of exported-object man pages with runnable examples above
the 80% BiocCheck threshold, resolving the R CMD BiocCheck ERROR.
MultiAssaySpatialExperiment 0.9.6
Documentation
- Reconciled the vignettes into a numbered, user-first set:
- 1. Introduction to MultiAssaySpatialExperiment --- overview, anatomy,
construction, accessors, subsetting, spatial operations, coercion, and a
compact quick-reference table.
- 2. Working with MultiAssaySpatialExperiment --- construction patterns,
subsetting, spatial annotation and aggregation, and labels <-> shapes.
- 3. MultiAssaySpatialExperiment use cases --- platform readers (Xenium,
Visium, Visium HD, CosMx, MERSCOPE) and real-world spatial workflows.
- Removed the Cheatsheet vignette (its chunks were globally unevaluated, which
BiocCheck flags); its quick-reference content is now a table in the
Introduction.
- Applied Bioconductor vignette conventions: numbered
VignetteIndexEntry,
BiocStyle::doc_date() compiled dates, and structured author metadata.