v4.0.4

[jiajic]

Breaking changes

• Remove do_manual_adj and image adjustment params from createGiottoVisiumObject()
• createGiottoVisiumObject() now creates giottoLargeImage for spatial images.
• exprCellCellcom() deprecated gene_set_* params removed

Bug fixes

• Fix metadata appending/sorting issues introduced by GiottoClass v0.1.3 (2024/01/12). Affected functions: addHMRF(), addFeatsPerc(), doScrubletDetect()
• findNetworkNeighbors() now has default spatial_network_name value of NULL
• get10Xmatrix() now obeys split_by_type = FALSE

Changes

• Deprecate set.seed in favor of seed param for binSpect()
• binSpect() now sets a seed by default for reproducibility
• pkgdown files moved to separate repo

Enhancements

• Use mixedsort() for unique clusters metadata info
• Remove unnecessary matrix densification and expose seed param in doScrubletDetect()
• Remove unnecessary matrix densification in makeSignMatrixRank()

[jiajic]

New issues are showing up with GHA testing for Mac and Windows, but not Linux. For unclear reasons, they are failing during due to not being able to install packages that are not even requirements setup-r-dependencies@v2 Check if package needs pandoc step. This is likely the result of a recent change in the github action.

[jiajic]

Turning off pandoc checking allows MacOS checking to pass, but Windows is still not passing.

This is related to UMAP differences that seem to have occurred for Linux, MacOS (and which have now been accounted for in tests), but not Windows so far.