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• 2024/07/11:
  • Use ward.D2 as the default hclust method (instead of ward.D).
  • Propagate hclust_method to the hclust functions.
  • Add and propagate dist_metrics (default is "euclidean") to the parallelDist functions.
  • Add custom_colors so cells can be highlighted with specific colors.
• 2024/08/05:
  • Add save_expr_cluster_rds to run() so expression data for clustering can be saved prior to be overwritten by denoised values.
• 2024/09/05:
  • Change the color scheme.
  • Tiny clusters (<1% of all tumor cells) are set to black, allowing other clusters to have distinct colors
• 2024/12/09:
  • Fix a rare issue where some cells seem unassigned to a cluster in row_groupings (are NA)