rliger Release v2.1.0

• Added centroidAlign() for new cell factor loading alignment method
• Added plotProportionBox() for visualizing compositional analysis
• Added plotClusterGeneViolin() for visualizing gene expression in clusters
• Added plotBarcodeRank() for basic QC visualization
• Added plotPairwiseDEGHeatmap() for visualizing pairwise DEG results
• Added plotGODot() for visualizing GO enrichment results
• Added calcNMI() for evaluating clustering results against ground truth
• Added ligerToH5AD() allowing reticulate/Python free export of liger object to H5AD format. This is presented in extension source code (i.e. not loaded with library(rliger)).
• Added organism support in runGeneralQC() and refined hemoglobin gene matching regex pattern.
• Optimized DE test memory usage scalability for both pseudo-bulk method and wilcoxon test
• Optimized plotProportionPie() by adding argument circleColors
• Optimized plotVolcano() text annotation positioning and gene highlighting logic.
• Optimized visualization function additional argument documentation
• Changed runMarkerDEG() and runPairwiseDEG() default method from "wilcoxon" to "pseudoBulk"
• Fixed runMarkerDEG(method = "pseudobulk") bug in assigning pseudo-replicates, and optimized error/warning signaling.
• Fixed bug in calcAlignment(), subsetMemLigerDataset(), cellMeta()
• Fixed bug in old version updating functions