Code

GiottoClass v0.4.0#241

Code

Merged

jiajic merged 166 commits intomaindrieslab/GiottoClass:mainfrom devdrieslab/GiottoClass:devCopy head branch name to clipboardOct 27, 2024

+5,194-3,697

Commits

Commits on Aug 28, 2024

• chore: gitignore pkgdown

  jiajic

  committed
  8638293

• Add: pip_packages param to allow repository selection when install conda env

  wwang-chcn

  committed
  01c6605

• Merge pull request #228 from wwang-chcn/dev

  Show description for 8c1c4f3
  jiajic

  authored
  8c1c4f3

Commits on Aug 29, 2024

• Fix functions to be generalizable for more datasets

  sjcshin

  committed
  e8858a3

Commits on Aug 30, 2024

• fix: dimnames/colnames generics

  jiajic

  committed
  56f92a1

• chore: update news

  jiajic

  committed
  1e5d90e

• Merge branch 'dev' into dev

  sjcshin

  authored
  93bfde8

• Merge pull request #232 from sjcshin/dev

  Show description for 52b57e0
  jiajic

  authored
  52b57e0

• fix: joinGiottoObject

  Show description for 8fd03d1
  jiajic

  committed
  8fd03d1

• Merge branch 'dev' of https://github.com/drieslab/GiottoClass into dev

  jiajic

  committed
  2065f9f

• chore: update news

  jiajic

  committed
  c92a079

• chore: bump version for dev

  jiajic

  committed
  52cf472

• chore: add initial join tests

  jiajic

  committed
  c60c130

• Update methods-plot.R

  jiajic

  committed
  704fe66

Commits on Sep 5, 2024

• enh: instructions() updates

  jiajic

  committed
  103b7e3

Commits on Sep 9, 2024

• fix: dummy spatlocs prov

  jiajic

  committed
  71ba5ce

• chore: update join code

  jiajic

  committed
  ee4abd0

• chore: add missing docs

  jiajic

  committed
  903cc30

• feat!: stop exporting deprecated accessors

  Show description for b4cf4d0
  jiajic

  committed
  b4cf4d0

• chore: document

  Show description for a89a310
  jiajic

  committed
  a89a310

• chore: update Seurat converter (NNnet) code

  Show description for cac3b0e
  jiajic

  committed
  cac3b0e

• chore: docs

  jiajic

  committed
  fdef7f4

Commits on Sep 10, 2024

• fix: prevent unintended init during load

  jiajic

  committed
  cc12fc6

• feat: accessor check_preqs param

  Show description for b0da883
  jiajic

  committed
  b0da883

• feat: initialize param for initialize()

  Show description for 8063777
  jiajic

  committed
  8063777

• feat: bracket and subset() for giotto

  jiajic

  committed
  d272f5d

• Merge pull request #234 from jiajic/subset

  Show description for 41f11f1
  jiajic

  authored
  41f11f1

Commits on Sep 11, 2024

• fix: expression matrix subsetting error

  jiajic

  committed
  235f5c5

• feat: [ and subset() for giotto

  jiajic

  committed
  36101ef

• chore: docs

  jiajic

  committed
  59d4d5a

• chore: bioc style

  jiajic

  committed
  15535d7

• Update methods-extract.R

  jiajic

  committed
  e7aaa6b

• fix: subset_giotto docs and implementation

  jiajic

  committed
  acfa06c

Commits on Sep 12, 2024

• chore: update for [ being internal

  jiajic

  committed
  5dc573d

• enh: allow giotto validity skipping using option

  jiajic

  committed
  461f302

• enh: add dims to print method

  jiajic

  committed
  c597dbc

• enh: as.list() for giotto

  jiajic

  committed
  02797ad

• fix: checking option default

  Show description for 4407875
  jiajic

  committed
  4407875

• fix?: try adding S3 as.list() generic

  Show description for 062ab56
  jiajic

  committed
  062ab56

• Revert "fix?: try adding S3 as.list() generic"

  Show description for 360bfe8
  jiajic

  committed
  360bfe8

Commits on Sep 16, 2024

• enh: return NA when unsupported class for nesting generics

  jiajic

  committed
  b4be762

• chore: docs

  jiajic

  committed
  24d08cd

• feat!: revert check_preqs in setters

  jiajic

  committed
  a2079c6

• enh: sliceGiotto() now sets the active feat/spat

  jiajic

  committed
  1529dde

• enh: add 'giotto.init' option

  jiajic

  committed
  1b7b78f

• enh: setGiotto() now only inits and checks at once all items in list are added

  jiajic

  committed
  180383b

• Update NEWS.md

  jiajic

  committed
  abd6f34

• enh: [, [[, $ methods

  jiajic

  committed
  38fd231

• chore: docs

  jiajic

  committed
  cd583f0

• fix: make dim red getter find defaults

  jiajic

  committed
  c1e2539

• enh: spatValues to also check spatlocs and dimreduc

  jiajic

  committed
  7ade099

• chore: docs

  jiajic

  committed
  82c3dc9

• fix: assertion check

  jiajic

  committed
  987ebc8

Commits on Sep 17, 2024

• fix: dbrkt filters need to be vectorized |

  jiajic

  committed
  68a41ba

Commits on Sep 18, 2024

• feat: experimental rbind for meta objects

  jiajic

  committed
  9094423

Commits on Sep 19, 2024

• feat: subset arg for spatIDs() and featIDs()

  jiajic

  committed
  dd23e43

• chore: docs

  jiajic

  committed
  8eded01

• chore: news

  jiajic

  committed
  f60ce8d

• feat: add NSE escape hatch as quote param

  jiajic

  committed
  984db56

• feat: negate param for interactive subset funs

  jiajic

  committed
  5ad0e25

Commits on Sep 23, 2024

• Enhance Seurat interoperability for Xenium dataset support

  iqraAmin

  committed
  91deb23

• Merge pull request #235 from iqraAmin/dev

  Show description for 1e95553
  jiajic

  authored
  1e95553

• fix: py init

  jiajic

  committed
  ddf59a3

Commits on Sep 24, 2024

• feat: drop arg for [[ subsetting

  jiajic

  committed
  5d212dc

• chore: docs

  jiajic

  committed
  6ce7299

• fix: export dollarnames

  jiajic

  committed
  f2f4e09

• remove calling to inexistent dataset "stxBrain"

  josschavezf

  committed
  e11dc15

Commits on Sep 25, 2024

• run devtools::document

  josschavezf

  committed
  3681f36

• add params description

  josschavezf

  committed
  a246648

• add params description

  josschavezf

  committed
  e917e56

• remove duplicated params

  josschavezf

  committed
  a02130e

• replace readGiottoInstructions -> instructions

  josschavezf

  committed
  72027b4

• add test using RDS method

  josschavezf

  committed
  9676ca2

• add overwrite = TRUE to solve test error

  josschavezf

  committed
  dec7d7d

• Merge pull request #236 from josschavezf/dev

  Show description for c0cca85
  josschavezf

  authored
  c0cca85

• try new workflow

  josschavezf

  committed
  ccee165

• Merge branch 'dev' of https://github.com/josschavezf/GiottoClass into dev

  josschavezf

  committed
  357a97b

• add packages

  josschavezf

  committed
  7e3c0fa

• remove reference to Giottovisuals function to avoid warning in rcmdcheck

  josschavezf

  committed
  ba03ade

• remove calling for Giotto

  josschavezf

  committed
  0fcfcec

• remove calling to GiottoVisuals

  josschavezf

  committed
  f61cbe5

• add returns value

  josschavezf

  committed
  5b67180

• add OS

  josschavezf

  committed
  ab21cb9

• install dev

  josschavezf

  committed
  a56d602

• remove calling to Giotto package

  josschavezf

  committed
  1872b98

• fix documentation warnings

  josschavezf

  committed
  dca0c4e

• change installation instruction

  josschavezf

  committed
  7de30e2

• run first bioccheck

  josschavezf

  committed
  dcc8ec5

Commits on Sep 26, 2024

• add returns value

  josschavezf

  committed
  a348a4a

• Merge pull request #237 from josschavezf/dev

  Show description for cf5558a
  josschavezf

  authored
  cf5558a

Commits on Sep 27, 2024

• fix: as.list docs

  jiajic

  committed
  fa02475

Commits on Sep 30, 2024

• change rcmdcheck run

  josschavezf

  committed
  65d9ab6

• update R version

  josschavezf

  committed
  222eb19

Commits on Oct 1, 2024

• Merge pull request #238 from josschavezf/dev

  Show description for 6ab02d4
  josschavezf

  authored
  6ab02d4

Commits on Oct 3, 2024

• enh: improve objHistory() printing

  jiajic

  committed
  70feef1

• chore: styling

  jiajic

  committed
  deaaab4

• change: deprecate and replace showProcessingSteps

  jiajic

  committed
  97431ac

• chore: param doc

  jiajic

  committed
  5f7645b

• enh: add param recording escape hatch

  jiajic

  committed
  1a94574

• chore: docs

  jiajic

  committed
  d337512

Commits on Oct 8, 2024

• enh: $<- for giotto

  jiajic

  committed
  ce1e3c0

• enh: nrow(), ncol(), dim() for giotto

  jiajic

  committed
  7930c7a

• enh: ext for affine2d

  jiajic

  committed
  69d008b

Commits on Oct 9, 2024

• enh: dimnames for giotto

  jiajic

  committed
  161e974

Commits on Oct 10, 2024

• fix: this error message didn't work

  Show description for 9262de3
  jiajic

  committed
  9262de3

• feat: splitGiotto

  jiajic

  committed
  69420a7

• Update NEWS.md

  jiajic

  committed
  d3d06c8

Commits on Oct 11, 2024

• chore: remove unneeded code

  jiajic

  committed
  1ccf2f5

• chore: remove unneeded code

  jiajic

  committed
  01b0a38

• Update join.R

  jiajic

  committed
  afe32e3

• enh: spatValues accesses multiple spat units

  jiajic

  committed
  9c34176

• fix: issue where image features are assumed to be points features

  jiajic

  committed
  cf7a633

• Update NEWS.md

  jiajic

  committed
  8bb1e8d

• chore: docs

  jiajic

  committed
  a32d893

Commits on Oct 13, 2024

• chore: remove unnecessary rd

  jiajic

  committed
  ef1fc36

• chore: docs

  jiajic

  committed
  cc94725

• chore: remove extra import tags

  jiajic

  committed
  1b2d85c

• chore: further cleanup imports

  jiajic

  committed
  776c602

• Update NAMESPACE

  jiajic

  committed
  bde44d2

• enh: [] for giottoImage and giottoLargeImage

  jiajic

  committed
  228fbb5

• enh: as.points for spatLocsObj

  jiajic

  committed
  f60422a

Commits on Oct 15, 2024

• feat: relate, +, -, symdif, intersect, union, snap

  jiajic

  committed
  7e161d2

• chore: docs

  jiajic

  committed
  ba2e552

• Update spat_binary_ops.Rd

  jiajic

  committed
  4e12bc0

• !feat: remove combineSpatialCellFeatureInfo()

  Show description for e0624c2
  jiajic

  committed
  e0624c2

• chore: move sp to suggests

  jiajic

  committed
  1194d1b

Commits on Oct 17, 2024

• enh: createGiottoLargeImage now works for all things rast does

  jiajic

  committed
  9e04dd8

• chore: docs

  jiajic

  committed
  f216181

• fix: createGiottoPolygonsFromMask() shift step functions now actually work as steps

  jiajic

  committed
  f4caa27

• chore: update news

  jiajic

  committed
  7f54f03

• feat: XY() and XY<-() for coord access

  jiajic

  committed
  2269520

Commits on Oct 18, 2024

• enh: feat meta + matrix joining can select ids

  Show description for 549d6e0
  jiajic

  committed
  549d6e0

Commits on Oct 21, 2024

• fix: ":all:" passing for subsetGiotto

  jiajic

  committed
  d6468bb

• fix: poly subsetting now matches spatlocs when possible

  jiajic

  committed
  f0f3092

• chore: docs

  jiajic

  committed
  1624544

• enh: relate method for giotto

  jiajic

  committed
  97a80c4

• chore: update relate docs

  jiajic

  committed
  d47a88c

Commits on Oct 22, 2024

• feat: doDeferred()

  jiajic

  committed
  8cc4dec

• Merge pull request #240 from jiajic/defer

  Show description for a6d1641
  jiajic

  authored
  a6d1641

• chore: docs

  jiajic

  committed
  d5be937

• chore: docs

  jiajic

  committed
  b89c9af

Commits on Oct 23, 2024

• chore: init 3d engine option

  jiajic

  committed
  ead8fae

• fix: subsetGiottoLocs() subsets to be inclusive

  jiajic

  committed
  be5db47

Commits on Oct 24, 2024

• Update NEWS.md

  jiajic

  committed
  ffde2f1

Commits on Oct 25, 2024

• chore: add some comments

  jiajic

  committed
  9df41f6

• fix: giottoAffineImage load after save

  jiajic

  committed
  3ad051a

• Update NEWS.md

  jiajic

  committed
  cea82c0

Commits on Oct 26, 2024

• feat: convHull()

  jiajic

  committed
  e553a5a

• chore: deps cleanup

  jiajic

  committed
  38f6fd7

• chore: docs

  jiajic

  committed
  0b426a9

• feat: area()

  jiajic

  committed
  7c6fb21

• Update NEWS.md

  jiajic

  committed
  9bf8d53

• fix: prevent terra namespace conflict

  jiajic

  committed
  84eaf28

Commits on Oct 27, 2024

• chore: styler

  jiajic

  committed
  7cc973c

• chore: docs

  jiajic

  committed
  f03d7a9

• fix: make sure images are updated after load

  jiajic

  committed
  18648b8

• fix: XY spatlocs method

  jiajic

  committed
  81b895f

• remove extraneous ...

  jiajic

  committed
  223bf46

• change: remove + - in favor of just union and erase

  Show description for 4696835
  jiajic

  committed
  4696835

• chore: docs update for convHull

  jiajic

  committed
  1a1c822

• chore: fix docs

  jiajic

  committed
  114f477

• Update NEWS.md

  jiajic

  committed
  ddb5a95

• Update DESCRIPTION

  jiajic

  committed
  edd1563

• Merge branch 'main' into dev

  jiajic

  committed
  ffcbd32

• chore: bump version and remove remotes for dev

  jiajic

  committed
  d15487d

• Revert "chore: bump version and remove remotes for dev"

  Show description for 23a475a
  jiajic

  committed
  23a475a