From 3d4e4179647197a9b431d823318f2c749300b11d Mon Sep 17 00:00:00 2001 From: Michael Totty Date: Wed, 20 Nov 2024 14:04:00 -0500 Subject: [PATCH] fixed NEWS.md so it shows up on website --- DESCRIPTION | 2 +- NEWS.md | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index dcef01c..22e771a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,6 @@ Package: SpotSweeper Title: Spatially-aware quality control for spatial transcriptomics Version: 1.3.1 Date: 2024-11-08 - Authors@R: c( person("Michael", "Totty", ,"mictott@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9292-8556")), @@ -52,3 +51,4 @@ Suggests: Config/testthat/edition: 3 VignetteBuilder: knitr LazyData: False +News: NEWS.md diff --git a/NEWS.md b/NEWS.md index 492d5fb..1db4bcf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,19 +1,19 @@ # SpotSweeper Package News -## Version 1.3.1 +# Version 1.3.1 -### Major Changes +## Major Changes - **Function Renaming**: The function `plotQC` has been renamed to `plotQCmetrics` to better reflect its purpose. The new function `plotQCmetrics` should be used moving forward. This change improves clarity in the package’s API by specifying that this function is designed for plotting QC metrics. -### New Features and Enhancements +## New Features and Enhancements - **`shape` argument**: Added a `shape` argument to `findArtifacts`, allowing users to specify the neighborhood shape as either `"hexagonal"` or `"square"` for local variance calculations. This enhancement provides flexibility for different spatial arrangements in spatial transcriptomics data. - **Updated `n_order` parameter**: Renamed the `n_rings` parameter to `n_order` in the `findArtifacts` function to better describe its purpose of specifying the N-order neighbors for local mitochondrial variance calculations. - **Parallelization**: Added a `workers` argument for parallel processing using `BiocParallel` in both `localOutlier` and `localVariance` functions. This allows for faster computation, particularly on larger datasets. -### Deprecations +## Deprecations - **`plotQC` Function Deprecated**: The `plotQC` function is now deprecated. While it remains available for backward compatibility, users are encouraged to transition to `plotQCmetrics`. Calling `plotQC` will display a warning, reminding users of the deprecation. This change is backward compatible; existing code using `plotQC` will still work but will show a warning. We recommend updating your code to use `plotQCmetrics` to avoid any issues in future versions where `plotQC` may be removed.