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mistyR 1.99.x

  • Enable signature extraction without intersecting targets.
  • Enable calculation of communities on non-square matrices.
  • Results are now stored in database instead of a folder.
  • Correlations are calculated alongside importances to give an intuition about the sign of the relationship.

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.