Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
Fig 9
(a) ISOMAP and diffusion map plots of the down-sampled subsets. Cells are color-coded by ClusterX clusters. Cluster IDs are labeled at the center of each cluster (b) Plots of the expression level of marker Perforin using ISOMAP and diffusion map. Estimated progression among annotated subsets γδ Vd+, γδ Vd−, CD8 Eff, NKT and NK are added on the plots. (c) The expression profiles of marker Perforin and GranzymeB for cluster 11, 12, 13, 14 and 15 are visualized on the second component of ISOMAP and diffusion map (reversed order). The regression line estimated using the generalized linear model (GLM) is added for each marker.