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GiottoClass v0.4.0 #241

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merged 166 commits into from
Oct 27, 2024
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8638293
chore: gitignore pkgdown
jiajic Aug 28, 2024
01c6605
Add: pip_packages param to allow repository selection when install co…
wwang-chcn Aug 28, 2024
8c1c4f3
Merge pull request #228 from wwang-chcn/dev
jiajic Aug 28, 2024
e8858a3
Fix functions to be generalizable for more datasets
sjcshin Aug 29, 2024
56f92a1
fix: dimnames/colnames generics
jiajic Aug 30, 2024
1e5d90e
chore: update news
jiajic Aug 30, 2024
93bfde8
Merge branch 'dev' into dev
sjcshin Aug 30, 2024
52b57e0
Merge pull request #232 from sjcshin/dev
jiajic Aug 30, 2024
8fd03d1
fix: `joinGiottoObject`
jiajic Aug 30, 2024
2065f9f
Merge branch 'dev' of https://github.com/drieslab/GiottoClass into dev
jiajic Aug 30, 2024
c92a079
chore: update news
jiajic Aug 30, 2024
52cf472
chore: bump version for dev
jiajic Aug 30, 2024
c60c130
chore: add initial join tests
jiajic Aug 30, 2024
704fe66
Update methods-plot.R
jiajic Aug 30, 2024
103b7e3
enh: `instructions()` updates
jiajic Sep 5, 2024
71ba5ce
fix: dummy spatlocs prov
jiajic Sep 9, 2024
ee4abd0
chore: update join code
jiajic Sep 9, 2024
903cc30
chore: add missing docs
jiajic Sep 9, 2024
b4cf4d0
feat!: stop exporting deprecated accessors
jiajic Sep 9, 2024
a89a310
chore: document
jiajic Sep 9, 2024
cac3b0e
chore: update Seurat converter (NNnet) code
jiajic Sep 9, 2024
fdef7f4
chore: docs
jiajic Sep 9, 2024
cc12fc6
fix: prevent unintended init during load
jiajic Sep 10, 2024
b0da883
feat: accessor `check_preqs` param
jiajic Sep 10, 2024
8063777
feat: `initialize` param for `initialize()`
jiajic Sep 10, 2024
d272f5d
feat: bracket and `subset()` for `giotto`
jiajic Sep 10, 2024
41f11f1
Merge pull request #234 from jiajic/subset
jiajic Sep 10, 2024
235f5c5
fix: expression matrix subsetting error
jiajic Sep 11, 2024
36101ef
feat: `[` and `subset()` for `giotto`
jiajic Sep 11, 2024
59d4d5a
chore: docs
jiajic Sep 11, 2024
15535d7
chore: bioc style
jiajic Sep 11, 2024
e7aaa6b
Update methods-extract.R
jiajic Sep 11, 2024
acfa06c
fix: subset_giotto docs and implementation
jiajic Sep 11, 2024
5dc573d
chore: update for `[` being internal
jiajic Sep 12, 2024
461f302
enh: allow giotto validity skipping using option
jiajic Sep 12, 2024
c597dbc
enh: add dims to print method
jiajic Sep 12, 2024
02797ad
enh: `as.list()` for `giotto`
jiajic Sep 12, 2024
4407875
fix: checking option default
jiajic Sep 12, 2024
062ab56
fix?: try adding S3 `as.list()` generic
jiajic Sep 12, 2024
360bfe8
Revert "fix?: try adding S3 `as.list()` generic"
jiajic Sep 12, 2024
b4be762
enh: return NA when unsupported class for nesting generics
jiajic Sep 16, 2024
24d08cd
chore: docs
jiajic Sep 16, 2024
a2079c6
feat!: revert `check_preqs` in setters
jiajic Sep 16, 2024
1529dde
enh: `sliceGiotto()` now sets the active feat/spat
jiajic Sep 16, 2024
1b7b78f
enh: add 'giotto.init' option
jiajic Sep 16, 2024
180383b
enh: `setGiotto()` now only inits and checks at once all items in lis…
jiajic Sep 16, 2024
abd6f34
Update NEWS.md
jiajic Sep 16, 2024
38fd231
enh: `[`, `[[`, `$` methods
jiajic Sep 16, 2024
cd583f0
chore: docs
jiajic Sep 16, 2024
c1e2539
fix: make dim red getter find defaults
jiajic Sep 16, 2024
7ade099
enh: spatValues to also check spatlocs and dimreduc
jiajic Sep 16, 2024
82c3dc9
chore: docs
jiajic Sep 16, 2024
987ebc8
fix: assertion check
jiajic Sep 16, 2024
68a41ba
fix: dbrkt filters need to be vectorized `|`
jiajic Sep 17, 2024
9094423
feat: experimental rbind for meta objects
jiajic Sep 18, 2024
dd23e43
feat: `subset` arg for `spatIDs()` and `featIDs()`
jiajic Sep 19, 2024
8eded01
chore: docs
jiajic Sep 19, 2024
f60ce8d
chore: news
jiajic Sep 19, 2024
984db56
feat: add NSE escape hatch as `quote` param
jiajic Sep 19, 2024
5ad0e25
feat: `negate` param for interactive subset funs
jiajic Sep 19, 2024
91deb23
Enhance Seurat interoperability for Xenium dataset support
iqraAmin Sep 23, 2024
1e95553
Merge pull request #235 from iqraAmin/dev
jiajic Sep 23, 2024
ddf59a3
fix: py init
jiajic Sep 23, 2024
5d212dc
feat: `drop` arg for `[[` subsetting
jiajic Sep 24, 2024
6ce7299
chore: docs
jiajic Sep 24, 2024
f2f4e09
fix: export dollarnames
jiajic Sep 24, 2024
e11dc15
remove calling to inexistent dataset "stxBrain"
josschavezf Sep 24, 2024
3681f36
run devtools::document
josschavezf Sep 25, 2024
a246648
add params description
josschavezf Sep 25, 2024
e917e56
add params description
josschavezf Sep 25, 2024
a02130e
remove duplicated params
josschavezf Sep 25, 2024
72027b4
replace readGiottoInstructions -> instructions
josschavezf Sep 25, 2024
9676ca2
add test using RDS method
josschavezf Sep 25, 2024
dec7d7d
add overwrite = TRUE to solve test error
josschavezf Sep 25, 2024
c0cca85
Merge pull request #236 from josschavezf/dev
josschavezf Sep 25, 2024
ccee165
try new workflow
josschavezf Sep 25, 2024
357a97b
Merge branch 'dev' of https://github.com/josschavezf/GiottoClass into…
josschavezf Sep 25, 2024
7e3c0fa
add packages
josschavezf Sep 25, 2024
ba03ade
remove reference to Giottovisuals function to avoid warning in rcmdcheck
josschavezf Sep 25, 2024
0fcfcec
remove calling for Giotto
josschavezf Sep 25, 2024
f61cbe5
remove calling to GiottoVisuals
josschavezf Sep 25, 2024
5b67180
add returns value
josschavezf Sep 25, 2024
ab21cb9
add OS
josschavezf Sep 25, 2024
a56d602
install dev
josschavezf Sep 25, 2024
1872b98
remove calling to Giotto package
josschavezf Sep 25, 2024
dca0c4e
fix documentation warnings
josschavezf Sep 25, 2024
7de30e2
change installation instruction
josschavezf Sep 25, 2024
dcc8ec5
run first bioccheck
josschavezf Sep 25, 2024
a348a4a
add returns value
josschavezf Sep 26, 2024
cf5558a
Merge pull request #237 from josschavezf/dev
josschavezf Sep 26, 2024
fa02475
fix: as.list docs
jiajic Sep 27, 2024
65d9ab6
change rcmdcheck run
josschavezf Sep 30, 2024
222eb19
update R version
josschavezf Sep 30, 2024
6ab02d4
Merge pull request #238 from josschavezf/dev
josschavezf Oct 1, 2024
70feef1
enh: improve `objHistory()` printing
jiajic Oct 3, 2024
deaaab4
chore: styling
jiajic Oct 3, 2024
97431ac
change: deprecate and replace showProcessingSteps
jiajic Oct 3, 2024
5f7645b
chore: param doc
jiajic Oct 3, 2024
1a94574
enh: add param recording escape hatch
jiajic Oct 3, 2024
d337512
chore: docs
jiajic Oct 3, 2024
ce1e3c0
enh: `$<-` for `giotto`
jiajic Oct 8, 2024
7930c7a
enh: `nrow()`, `ncol()`, `dim()` for `giotto`
jiajic Oct 8, 2024
69d008b
enh: ext for affine2d
jiajic Oct 8, 2024
161e974
enh: dimnames for `giotto`
jiajic Oct 9, 2024
9262de3
fix: this error message didn't work
jiajic Oct 10, 2024
69420a7
feat: `splitGiotto`
jiajic Oct 10, 2024
d3d06c8
Update NEWS.md
jiajic Oct 10, 2024
1ccf2f5
chore: remove unneeded code
jiajic Oct 11, 2024
01b0a38
chore: remove unneeded code
jiajic Oct 11, 2024
afe32e3
Update join.R
jiajic Oct 11, 2024
9c34176
enh: spatValues accesses multiple spat units
jiajic Oct 11, 2024
cf7a633
fix: issue where image features are assumed to be points features
jiajic Oct 11, 2024
8bb1e8d
Update NEWS.md
jiajic Oct 11, 2024
a32d893
chore: docs
jiajic Oct 11, 2024
ef1fc36
chore: remove unnecessary rd
jiajic Oct 13, 2024
cc94725
chore: docs
jiajic Oct 13, 2024
1b2d85c
chore: remove extra import tags
jiajic Oct 13, 2024
776c602
chore: further cleanup imports
jiajic Oct 13, 2024
bde44d2
Update NAMESPACE
jiajic Oct 13, 2024
228fbb5
enh: `[]` for `giottoImage` and `giottoLargeImage`
jiajic Oct 13, 2024
f60422a
enh: as.points for spatLocsObj
jiajic Oct 13, 2024
7e161d2
feat: `relate`, `+`, `-`, `symdif`, `intersect`, `union`, `snap`
jiajic Oct 15, 2024
ba2e552
chore: docs
jiajic Oct 15, 2024
4e12bc0
Update spat_binary_ops.Rd
jiajic Oct 15, 2024
e0624c2
!feat: remove `combineSpatialCellFeatureInfo()`
jiajic Oct 15, 2024
1194d1b
chore: move sp to suggests
jiajic Oct 15, 2024
9e04dd8
enh: `createGiottoLargeImage` now works for all things rast does
jiajic Oct 17, 2024
f216181
chore: docs
jiajic Oct 17, 2024
f4caa27
fix: createGiottoPolygonsFromMask() shift step functions now actually…
jiajic Oct 17, 2024
7f54f03
chore: update news
jiajic Oct 17, 2024
2269520
feat: `XY()` and `XY<-()` for coord access
jiajic Oct 17, 2024
549d6e0
enh: feat meta + matrix joining can select ids
jiajic Oct 18, 2024
d6468bb
fix: ":all:" passing for subsetGiotto
jiajic Oct 21, 2024
f0f3092
fix: poly subsetting now matches spatlocs when possible
jiajic Oct 21, 2024
1624544
chore: docs
jiajic Oct 21, 2024
97a80c4
enh: relate method for `giotto`
jiajic Oct 21, 2024
d47a88c
chore: update relate docs
jiajic Oct 21, 2024
8cc4dec
feat: `doDeferred()`
jiajic Oct 22, 2024
a6d1641
Merge pull request #240 from jiajic/defer
jiajic Oct 22, 2024
d5be937
chore: docs
jiajic Oct 22, 2024
b89c9af
chore: docs
jiajic Oct 22, 2024
ead8fae
chore: init 3d engine option
jiajic Oct 23, 2024
be5db47
fix: subsetGiottoLocs() subsets to be inclusive
jiajic Oct 23, 2024
ffde2f1
Update NEWS.md
jiajic Oct 24, 2024
9df41f6
chore: add some comments
jiajic Oct 25, 2024
3ad051a
fix: giottoAffineImage load after save
jiajic Oct 25, 2024
cea82c0
Update NEWS.md
jiajic Oct 25, 2024
e553a5a
feat: `convHull()`
jiajic Oct 26, 2024
38f6fd7
chore: deps cleanup
jiajic Oct 26, 2024
0b426a9
chore: docs
jiajic Oct 26, 2024
7c6fb21
feat: `area()`
jiajic Oct 26, 2024
9bf8d53
Update NEWS.md
jiajic Oct 26, 2024
84eaf28
fix: prevent terra namespace conflict
jiajic Oct 26, 2024
7cc973c
chore: styler
jiajic Oct 27, 2024
f03d7a9
chore: docs
jiajic Oct 27, 2024
18648b8
fix: make sure images are updated after load
jiajic Oct 27, 2024
81b895f
fix: XY spatlocs method
jiajic Oct 27, 2024
223bf46
remove extraneous ...
jiajic Oct 27, 2024
4696835
change: remove + - in favor of just union and erase
jiajic Oct 27, 2024
1a1c822
chore: docs update for convHull
jiajic Oct 27, 2024
114f477
chore: fix docs
jiajic Oct 27, 2024
ddb5a95
Update NEWS.md
jiajic Oct 27, 2024
edd1563
Update DESCRIPTION
jiajic Oct 27, 2024
ffcbd32
Merge branch 'main' into dev
jiajic Oct 27, 2024
d15487d
chore: bump version and remove remotes for dev
jiajic Oct 27, 2024
23a475a
Revert "chore: bump version and remove remotes for dev"
jiajic Oct 27, 2024
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204 changes: 204 additions & 0 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,204 @@
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [dev]
pull_request:
branches: [dev]

name: R-CMD-check.yaml

permissions: read-all

jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}

name: ${{ matrix.config.os }} (${{ matrix.config.r }})

strategy:
fail-fast: false
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'release'}

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true



- name: Install reticulate
run: |
Rscript -e "install.packages('reticulate')"

- name: Create miniconda
run: |
Rscript -e "reticulate::install_miniconda()"
Rscript -e "reticulate::conda_install(packages = 'scipy')"

- name: Install pak
run: |
Rscript -e "install.packages('pak')"

- name: Install remotes
run: |
Rscript -e "install.packages('remotes')"

- name: Install GiottoUtils
run: |
Rscript -e "remotes::install_github('drieslab/GiottoUtils@dev')"

- name: Install GiottoData
run: |
Rscript -e "remotes::install_github('drieslab/GiottoData')"

- name: Install rcmdcheck
run: |
Rscript -e "install.packages('rcmdcheck')"

- name: Install knitr
run: |
Rscript -e "install.packages('knitr')"

- name: Install rmarkdown
run: |
Rscript -e "install.packages('rmarkdown')"

- name: Install testthat
run: |
Rscript -e "install.packages('testthat')"

- name: Install BiocCheck
run: |
Rscript -e "install.packages('BiocManager')"
Rscript -e "BiocManager::install('BiocCheck')"

- name: Install dbscan
run: |
Rscript -e "BiocManager::install('dbscan')"

- name: Install deldir
run: |
Rscript -e "BiocManager::install('deldir')"

- name: Install igraph
run: |
Rscript -e "BiocManager::install('igraph')"

- name: Install magick
run: |
Rscript -e "BiocManager::install('magick')"

- name: Install matrixStats
run: |
Rscript -e "BiocManager::install('matrixStats')"

- name: Install sp
run: |
Rscript -e "BiocManager::install('sp')"

- name: Install terra
run: |
Rscript -e "BiocManager::install('terra')"

- name: Install scattermore
run: |
Rscript -e "install.packages('scattermore')"

- name: Install exactextractr
run: |
Rscript -e "install.packages('exactextractr')"

- name: Install future.apply
run: |
Rscript -e "BiocManager::install('future.apply')"

- name: Install stars
run: |
Rscript -e "BiocManager::install('stars')"

- name: Install qs
run: |
Rscript -e "BiocManager::install('qs')"

- name: Install RTriangle
run: |
Rscript -e "BiocManager::install('RTriangle')"

- name: Install geometry
run: |
Rscript -e "BiocManager::install('geometry')"

- name: Install Seurat
run: |
Rscript -e "BiocManager::install('Seurat')"

- name: Install chihaya
run: |
Rscript -e "BiocManager::install('chihaya')"

- name: Install DelayedArray
run: |
Rscript -e "BiocManager::install('DelayedArray')"

- name: Install DelayedMatrixStats
run: |
Rscript -e "BiocManager::install('DelayedMatrixStats')"

- name: Install HDF5Array
run: |
Rscript -e "BiocManager::install('HDF5Array')"

- name: Install rgl
run: |
Rscript -e "BiocManager::install('rgl')"

- name: Install rhdf5
run: |
Rscript -e "BiocManager::install('rhdf5')"

- name: Install S4Vectors
run: |
Rscript -e "BiocManager::install('S4Vectors')"

- name: Install ScaledMatrix
run: |
Rscript -e "BiocManager::install('ScaledMatrix')"

- name: Install SingleCellExperiment
run: |
Rscript -e "BiocManager::install('SingleCellExperiment')"

- name: Install SpatialExperiment
run: |
Rscript -e "BiocManager::install('SpatialExperiment')"

- name: Install STexampleData
run: |
Rscript -e "BiocManager::install('STexampleData')"

- name: Install SummarizedExperiment
run: |
Rscript -e "BiocManager::install('SummarizedExperiment')"

- name: Run BiocCheck
run: |
Rscript -e "BiocCheck::BiocCheck()"

- name: Run rcmdcheck
run: |
Rscript -e "rcmdcheck::rcmdcheck()"
2 changes: 1 addition & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -8,5 +8,5 @@ inst/doc
.Rprofile
docs
codecov.yml

pkgdown
cell_rna*
19 changes: 11 additions & 8 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: GiottoClass
Title: Giotto Suite object definitions and framework
Version: 0.3.5
Version: 0.4.0
Authors@R: c(
person("Ruben", "Dries", email = "[email protected]",
role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
Expand All @@ -26,15 +26,13 @@ Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
base (>= 4.0.1),
utils (>= 4.0.1),
R (>= 4.0.1),
R (>= 4.4.1)
Imports:
checkmate,
data.table (>= 1.12.2),
dbscan (>= 1.1-3),
deldir (>= 1.0.6),
GiottoUtils (>= 0.1.10),
GiottoUtils (>= 0.2.0),
graphics,
grDevices,
igraph (>= 1.2.4.1),
Expand All @@ -43,9 +41,8 @@ Imports:
matrixStats (>= 0.55.0),
methods,
reticulate (>= 1.25),
sp,
stats,
terra (>= 1.7-39)
terra (>= 1.7-41)
Suggests:
Biobase,
chihaya,
Expand All @@ -57,7 +54,6 @@ Suggests:
HDF5Array (>= 1.18.1),
knitr,
plotly,
R.utils,
raster,
remotes,
reshape2,
Expand All @@ -73,6 +69,7 @@ Suggests:
SeuratObject,
sf,
SingleCellExperiment,
sp,
SpatialExperiment,
stars,
STexampleData,
Expand Down Expand Up @@ -107,9 +104,12 @@ Collate:
'interoperability.R'
'join.R'
'methods-IDs.R'
'methods-XY.R'
'methods-affine.R'
'methods-area.R'
'methods-centroids.R'
'methods-coerce.R'
'methods-convHull.R'
'methods-copy.R'
'methods-crop.R'
'methods-dims.R'
Expand All @@ -124,6 +124,7 @@ Collate:
'methods-plot.R'
'methods-rbind.R'
'methods-reconnect.R'
'methods-relate.R'
'methods-rescale.R'
'methods-setGiotto.R'
'methods-shear.R'
Expand All @@ -140,8 +141,10 @@ Collate:
'slot_check.R'
'slot_list.R'
'slot_show.R'
'spatial_binary_ops.R'
'spatial_query.R'
'spatial_structures.R'
'split.R'
'stitch_coordinates.R'
'subset.R'
'suite_reexports.R'
Expand Down
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