========================= *** Version 1.4.0 *** ------------------------- CATALYST now provides a series of visualization tools for differential analysis. These have been adapted from Nowicka M, Krieg C, Weber LM et al. "CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets" F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.2) and may be used in conjunction with Weber L (2018) "diffcyt: differential discovery in high-dimensional cytometry via high-resolution clustering" R package version 0.99.11, https://github.com/lmweber/diffcyt -------------------------------------------------- o Data returned by & used throughout differential analysis are held in objects of the 'daFrame-class' o The following functions are newly available: - plotCounts(), plotMDS(), plotExprs(), plotMedsExprs(): > general overview of data features - plotNRS(): > non-redundancy scores - tSNE(), plotSNE(): > run & visualize t-SNE - cluster(), mergeClusters(): > FlowSOM clustering, ConsensusClusterPlus meta-clustering, and manual cluster merging - plotCodes(): > PCA & t-SNE of SOM codes - plotAbundances(): > relative cluster abundances - plotClusterHeatmap(), plotDiffHeatmap() > ComplexHeatmap's summarizing clustering, meta-clustering & differential analysis results