Fig. 2
From: Reconstructing cell cycle pseudo time-series via single-cell transcriptome data
Illustration and evaluation of reCAT using the mESC-SMARTer data. a PCA visualization of mESC-SMARTer data using expression profiles of the Cyclebase genes (378). Each single cell is colored according to its experimentally determined cell cycle stage. A cycle linking eight black triangles represents the shortest traveling salesman cycle of eight cluster means, as computed by reCAT. b The bar plot at the top shows the composition of single cells at each predicted cell cycle phase. The jitter scatter plot at the bottom panel shows how well the ordered clusters are correlated with the known cell cycle stage labels. c The correlation-scores for various cluster numbers, between generated cell cycle time-series and experimentally determined cell cycle stage labels, are shown for the consensus-TSP algorithm, the arbitrary insertion algorithm for TSP, and Oscope. For each cluster number ‘k’, 200 runs of the arbitrary insertion algorithms were combined to compute and plot means and standard deviations (error bars). d Comparison of correlation-scores and change-index values for the time-series generated by reCAT, SCUBA, Monocle, TSCAN, Wish. /Wand., and DPT, using expression of the Cyclebase genes on mESC-SMARTer data
