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Merge remote-tracking branch 'origin/suite_dev' into db
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Ed2uiz committed Jul 29, 2024
2 parents 802b98f + efd44a4 commit 7697019
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17 changes: 10 additions & 7 deletions DESCRIPTION
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Package: Giotto
Title: Spatial Single-Cell Transcriptomics Toolbox
Version: 4.0.8
Version: 4.1.0
Authors@R: c(
person("Ruben", "Dries", email = "[email protected]",
role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
Expand All @@ -25,13 +25,13 @@ Encoding: UTF-8
LazyData: true
URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
BugReports: https://github.com/drieslab/Giotto/issues
RoxygenNote: 7.3.1
RoxygenNote: 7.3.2
Depends:
base (>= 4.1.0),
utils (>= 4.1.0),
R (>= 4.1.0),
methods,
GiottoClass (>= 0.3.1)
GiottoClass (>= 0.3.2)
Imports:
BiocParallel,
BiocSingular,
Expand All @@ -40,9 +40,8 @@ Imports:
data.table (>= 1.12.2),
dbscan (>= 1.1-3),
ggplot2 (>= 3.1.1),
ggrepel,
GiottoUtils (>= 0.1.8),
GiottoVisuals (>= 0.2.2),
GiottoUtils (>= 0.1.9),
GiottoVisuals (>= 0.2.4),
igraph (>= 1.2.4.1),
jsonlite,
limma,
Expand Down Expand Up @@ -132,10 +131,14 @@ Remotes:
drieslab/GiottoClass,
drieslab/GiottoVisuals
Collate:
'ONTraC_wrapper.R'
'auxiliary_giotto.R'
'cell_segmentation.R'
'clustering.R'
'convenience.R'
'convenience_cosmx.R'
'convenience_general.R'
'convenience_visiumHD.R'
'convenience_xenium.R'
'cross_section.R'
'dd.R'
'differential_expression.R'
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22 changes: 21 additions & 1 deletion NAMESPACE
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# Generated by roxygen2: do not edit by hand

S3method(.DollarNames,CosmxReader)
S3method(.DollarNames,VisiumHDReader)
S3method(.DollarNames,XeniumReader)
export("%>%")
export("activeFeatType<-")
export("activeSpatUnit<-")
Expand Down Expand Up @@ -149,9 +152,9 @@ export(crossSectionFeatPlot)
export(crossSectionFeatPlot3D)
export(crossSectionPlot)
export(crossSectionPlot3D)
export(density)
export(detectSpatialCorFeats)
export(detectSpatialCorFeatsMatrix)
export(detectSpatialCorGenes)
export(detectSpatialPatterns)
export(dimCellPlot)
export(dimCellPlot2D)
Expand Down Expand Up @@ -235,6 +238,7 @@ export(getGEFtxCoords)
export(getGiottoImage)
export(getMultiomics)
export(getNearestNetwork)
export(getONTraCv1Input)
export(getPolygonInfo)
export(getRainbowColors)
export(getSpatialEnrichment)
Expand All @@ -256,7 +260,11 @@ export(giottoToSpatialExperiment)
export(heatmSpatialCorFeats)
export(heatmSpatialCorGenes)
export(hexVertices)
export(hist)
export(hyperGeometricEnrich)
export(identifyTMAcores)
export(importCosMx)
export(importVisiumHD)
export(initHMRF_V2)
export(insertCrossSectionFeatPlot3D)
export(insertCrossSectionSpatPlot3D)
Expand All @@ -266,6 +274,7 @@ export(jackstrawPlot)
export(joinGiottoObjects)
export(loadGiotto)
export(loadHMRF)
export(loadOntraCResults)
export(makePseudoVisium)
export(makeSignMatrixDWLS)
export(makeSignMatrixDWLSfromMatrix)
Expand All @@ -285,8 +294,10 @@ export(pieCellTypesFromEnrichment)
export(plotCCcomDotplot)
export(plotCCcomHeatmap)
export(plotCPF)
export(plotCTCompositionInNicheCluster)
export(plotCellProximityFeatSpot)
export(plotCellProximityFeats)
export(plotCellTypeNTScore)
export(plotCellTypesFromEnrichment)
export(plotCombineCCcom)
export(plotCombineCellCellCommunication)
Expand All @@ -301,6 +312,7 @@ export(plotInteractive3D)
export(plotInteractivePolygons)
export(plotMetaDataCellsHeatmap)
export(plotMetaDataHeatmap)
export(plotNicheClusterConnectivity)
export(plotPCA)
export(plotPCA_2D)
export(plotPCA_3D)
Expand All @@ -315,10 +327,13 @@ export(plotUMAP)
export(plotUMAP_2D)
export(plotUMAP_3D)
export(polyStamp)
export(print.combIcfObject)
export(print.icfObject)
export(processGiotto)
export(prov)
export(rankEnrich)
export(rankSpatialCorGroups)
export(read10xAffineImage)
export(readCellMetadata)
export(readDimReducData)
export(readExprData)
Expand Down Expand Up @@ -485,8 +500,11 @@ export(viewHMRFresults3D)
export(viewHMRFresults_V2)
export(violinPlot)
export(wrap)
export(writeChatGPTqueryDEG)
export(writeGiottoLargeImage)
export(writeHMRFresults)
exportMethods("$")
exportMethods("$<-")
exportMethods(interpolateFeature)
import(GiottoClass)
import(GiottoUtils)
Expand Down Expand Up @@ -585,6 +603,7 @@ importFrom(GiottoClass,createSpatialNetwork)
importFrom(GiottoClass,createSpatialWeightMatrix)
importFrom(GiottoClass,crop)
importFrom(GiottoClass,cropGiottoLargeImage)
importFrom(GiottoClass,density)
importFrom(GiottoClass,distGiottoImage)
importFrom(GiottoClass,estimateImageBg)
importFrom(GiottoClass,ext)
Expand Down Expand Up @@ -619,6 +638,7 @@ importFrom(GiottoClass,giottoToSeuratV4)
importFrom(GiottoClass,giottoToSeuratV5)
importFrom(GiottoClass,giottoToSpatialExperiment)
importFrom(GiottoClass,hexVertices)
importFrom(GiottoClass,hist)
importFrom(GiottoClass,installGiottoEnvironment)
importFrom(GiottoClass,instructions)
importFrom(GiottoClass,joinGiottoObjects)
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27 changes: 27 additions & 0 deletions NEWS.md
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# Giotto 4.1.0 TBD

## Bug fixes
* Fix error in `plotInteractivePolygons()` when providing a spatial plot with a continuous scale [#964](https://github.com/drieslab/Giotto/issues/964) by jweis3
* Fix error in DWLS `find_dampening_constant()` when `S[subset, ]` produces only 1 gene.
* Fix error in `interpolateFeatures()` where feature names with `-` or starting with numbers did not work

## New
* `read10xAffineImage()` for reading 10x affine transformed images
* Several modular importer functions

# Giotto 4.0.9

## Breaking changes
* Deprecated `detectSpatialCorGenes()` removed. Use `detectSpatialCorFeats()` instead
* Deprecated `findInteractionChangedGenes()` removed. Use `findInteractionChangedFeats()` instead
* Deprecated `findCellProximityGenes()` removed. Use `findInteractionChangedFeats()` instead

## Bug fixes
* Add catch in `runPCAprojectionBatch()` for when ncp requested exceeds number of feats used
* Make `spatCellCellcom()` respect `verbose` flag [#949](https://github.com/drieslab/Giotto/issues/949) by rbutleriii

## Enhancements
* `print()` methods for `icfObject` and `combIcfObject`

## Changes
* require GiottoUtils (>= 0.1.9)

# Giotto 4.0.8 (2024/05/22)

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