scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
Fig 3
Two-dimensional scatter plots of the embedding from the three methods that calculate the similarity between contact matrices, including InnerProduct, fastHiCRep and Selfish.
(Dataset: Nagano et al., 2017). (a) Two-dimensional projection from InnerProduct and MDS shows a clear circular pattern along the four stages of cell cycle. (b) Two-dimensional projection using fastHiCRep and MDS does not show clear separation between the four stages of cell cycle. (c) Two-dimensional projection using Selfish and MDS does not show clear separation between the four stages of cell cycle. (d) Evaluating the three embedding methods in a cell-cycle phasing task by ACROC. The ACROC values from InnerProduct, fastHiCRep and Selfish are 0.904, 0.858 and 0.642, respectively.