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Giotto 4.1.3 #1057
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Giotto 4.1.3 #1057
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Suite devfix: allow instructions passing for Xenium conv.
loss of igprah call in identifying TMA
update R version
chore: move some deps to suggests
* remove deprecated `PAGEEnrich()`. Use `runPAGEEnrich()` instead * remove deprecated `rankEnrich()`. Use `runRankEnrich()` instead * remove deprecated `hyperGeometricEnrich()`. Use `runHyperGeometricEnrich()` instead * remove deprecated `createSpatialEnrich()`. Use `runSpatialEnrich()` instead * remove deprecated `heatmSpatialCorGenes()`. Use `heatmSpatialCorFeats()` instead * remove deprecated `runPAGEEnrich_OLD()`. Use `runPAGEEnrich()` instead * update PAGE example * start on reshape2 removal
- fix `findICFSpot()` example
updates for jackstraw
fix: seed setting
fix warning
!feat: remove re-export of combineSpatialCellFeatureInfo()
fix: doKmeans
fix: `doHclust()`
chore: deprecations for normalizeGiotto
- has minimal nodes to not be considerd disconnected - now repairs split cores
- change arg repair_split_cores to join_split_cores - add join_tolerance param for area allowed after joining to prevent joins of full cores pairs when the array has very small gutter space.
Suite dev
update news
chore: return remotes
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Updates since 4.1.0:
Breaking changes
PAGEEnrich()
. UserunPAGEEnrich()
insteadrankEnrich()
. UserunRankEnrich()
insteadhyperGeometricEnrich()
. UserunHyperGeometricEnrich()
insteadcreateSpatialEnrich()
. UserunSpatialEnrich()
insteadheatmSpatialCorGenes()
. UseheatmSpatialCorFeats()
insteadrunPAGEEnrich_OLD()
. UserunPAGEEnrich()
insteaddo_pca
,expression_values
,feats_to_use
args fromrunGiottoHarmony()
. Running PCA during theharmony::RunHarmony()
call is deprecated.Bug fixes
processGiotto()
can now skip adjust step by defaultgiottoInstructions
passing for Xenium convenience functionsChanges
runWNN()
andrunIntegratedUMAP()
arguments were updated to make the function flexible to handle any number of modalities.jackstrawPlot()
to make more flexible and efficient. Changed default params forscaling
,centering
, andfeats_to_use
to matchrunPCA()
runtSNE()
to error to avoid accidentally wiping thegiotto
object.limma
,plotly
, andRtsne
moved to Suggestsprogressr
andjsonlite
dependencies to GiottoUtils v0.1.12reshape2
dependency.screePlot()
name
in favor ofdim_reduction_name
paramEnhancements
'quantile'
normalization method tonormalizeGiotto()
New
giottoToAnndataZarr()
to create a local anndata zarr folder and interact with the vitessceR package.reduceDims()
API function for dimension reductionsrunNMF()
implementation that works via RcppMLidentifyTMAcores()
for assigning IDs to tissue microarray spatial data.labelTransfer()
for transferring labels between giotto objects or subsets thereof. SupercedesdoClusterProjection()