NEWS.md

In saezlab/misty: Multiview Intercellular SpaTial modeling framework

mistyR 1.9.x

mistyR 1.8.1

• Requires dplyr >=1.1.0 due to change of sorting order in arrange()

mistyR 1.8.0

• Release version for Bioconductor 3.17.

mistyR 1.6.1

• Discontinue the use of .data due to its deprecation since tidyselect 1.2.0.
• Update minimum required versions for some tidyverse related packages due to function deprecation.

mistyR 1.6.0

• Release version for Bioconductor 3.16. See changes for 1.5.x.

mistyR 1.5.x

• Added different modeling functions. Might not be completely backwards compatible!

mistyR 1.4.0

• Release version for Bioconductor 3.15. See changes for 1.3.x.

mistyR 1.3.x

• Switched from Louvain to Leiden algorithm for community detection (requires igraph >= 1.2.7).
• The metamodel is now build by ridge regression. Intercept p-values are not calculated, the values are set to NA for backwards compatibility.
• Unique value error for cv folds is downgraded to warning.
• Prefix can be added to the column names generated by the fucntions add_juxtaview and add_paraview. This allows modeling the maker expression by its own juxtaview and paraview.
• Bug fixes.

mistyR 1.2.1

• Fixed a separator issue in results aggregation and signature generation that might cause issues with variable names containing "_".

mistyR 1.2.0

• Release version for Bioconductor 3.14. See changes for 1.1.x.

mistyR 1.1.x

• Added functions for view manipulation, including view filtering and marker selection.
• Added functions for performance, contribution and importance signature extraction from results.
• Aggregation and signature generation is generalized for samples with non-identical targets by working on the intersection.
• Modeling of intraview can be bypassed.
• Added families of distances to calculate paraview.
• Paraview can exlcude measurements within a used defined zone of indifference around each spatial unit.
• Improved plotting control.
• Complete test coverage.

IMPORTANT: R2 is now reported in percentages for intra, multi and gain. Collecting results from running mistyR < 1.1.11 will lead to miscalculation of gain.R2. Update the performance.txt files by multiplying the values in columns intra.R2 and multi.R2 by 100.

mistyR 1.0.3

• Fixed display of messages and progress during view generation.
• Improved plotting control and display.
• Fixed handling of NaN in results.
• Vignette output switched from BiocStyle to rmarkdown for pdfs due to BiocStyle issue.

mistyR 1.0.2

• Bugfix: models built with different parameters stored and retrieved from the same cache file.
• Avoid calls to os-dependent file.info in tests.

mistyR 1.0.1

• Bugfix: passing arguments to ranger.
• Warnings on clearing nonexistent cache folders and tests of performance.
• Increased test coverage.

mistyR 1.0.0

• Release version for Bioconductor 3.13.

mistyR 0.99.11

• Fixed a bug in Nystrom approximation for creating paraview.
• Added a suite of tests with high coverage.
• Cleaner cache control.

mistyR 0.99.9

Revisions requested by Bioconductor

• Removed magrittr from dependencies. Reexported pipe operator. Removed from examples.
• Caching turned off by default.
• Added parameter for appending performance and coefficient files in run_misty.
• Internal functions in views.R are now explicit.
• Removed alternatives and additional examples for function use from documentation.
• Removed redundant messages, escalated to warnings where required.
• run_misty cleans up empty cache directories.
• Vignette compatibility with the new release of SpatialExperiment.
• Remove Seurat vignette from package due to missing hdf5r binary for R 4.1 on CRAN for MacOS.

Other changes

• README.md figures moved to the cloud.
• All passed paths and cache location are normalized.
• Changes in the mistyR vignette to reflect changes to insilico evaluation from the paper.

mistyR 0.99.0

• Version with vignettes ready to submit to Bioconductor.

mistyR 0.1.0 (MISTy)

• Initial beta release of mistyR (named as MISTy) with function documentation.

saezlab/misty documentation built on March 25, 2024, 4:11 p.m.