Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
Fig 5
Comparison of dimensionality reduction methods.
PCA, ISOMAP and t-SNE are performed on the CD14−CD19− PBMCs dataset and the CD4+ T cell dataset, respectively. In each panel, Cells are plotted using the first two dimensions of the dimensionality-transformed data and color coded by gated populations. (a) Plot of manually gated CD4+, CD8+, γδT, CD3+CD56+ NKT and CD3−CD56+ NK cell populations from the CD14−CD19− PBMCs dataset using PCA, ISOMAP, and t-SNE. (b) Plot of manually gated naïve (CD45RA+CCR7+CD45RO-), TH1 (IFN-γ+), TH17 (IL-17A+) and TFH (CXCR5hiPD-1hi) cell populations from the CD4+ T cell dataset using PCA, ISOMAP, and t-SNE.