Giotto 4.1.3 #1057
Merged
Giotto 4.1.3 #1057
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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_useargs fromrunGiottoHarmony(). Running PCA during theharmony::RunHarmony()call is deprecated.Bug fixes
processGiotto()can now skip adjust step by defaultgiottoInstructionspassing 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_useto matchrunPCA()runtSNE()to error to avoid accidentally wiping thegiottoobject.limma,plotly, andRtsnemoved to Suggestsprogressrandjsonlitedependencies to GiottoUtils v0.1.12reshape2dependency.screePlot()namein favor ofdim_reduction_nameparamEnhancements
'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()