Seurat dependency set to 5.3.0 at minimum to avoid the installation of leidenalg python package when selecting the Leiden method for clustering.
The clusters and ncells elements of the @cnacalling slot in muscadet objects are now updated during the cnaCalling() function right after some clusters need to be skipped due to not enough data. This resolves discordance between clusters and ncells elements with other @cnacalling elements, and avoids issues in plotting functions.
The CNA calling functions (assignClusters(), mergeCounts() and cnaCalling() now all in cnaCalling.R) now include a reset of the @cnacalling slot of the muscadet object, to avoid discordance between results if clusters or parameters are changed in between the different steps of the CNA calling.
Documentation
Documentation added to clusterMuscadet() and cluster_seurat() for Leiden clustering algorithm recommendation when using the Seurat method.
muscadet 0.1.1
Bug Fixes
Fix issue of heatmapMuscadet() crashing corner case: heatmapMuscadet() no longer crashes when averages=TRUE for one cluster only (monoclonal samples).
Fix issue of heatmapMuscadet() with a wrong cluster order after Seurat clustering: cluster_seurat() and imputeClusters() now return sorted clusters vectors, from 1 to n, cells with imputed clusters are therefore placed at the end of each cluster group.
Fix issue of wrong silhouette computation (due to clusters sorting changes): clusters are ordered according to the distance matrix order of cells used for silhouette computation, giving the correct silhouette scores.
The SeuratObject package is now attached along with muscadetto easily use Cells() and Features() methods on muscadet objects.
