Fig. 5: Analysis of cell trajectory in imputed data from different methods.
From: Leveraging data-driven self-consistency for high-fidelity gene expression recovery
PHATE results from the reference data (first column), observed data (second column), imputed data from MAGIC, mcImpute, and SERM (columns 3–5) for a zebrafish development data and b EB differentiation data. The observed data were created by sampling the reference data at 0.1% efficiency for both datasets. All the trajectories are better visualized in SERM imputed data. MAGIC and mcImpute distort the data in both cases, whereas SERM retains the consistency of the data intact in both cases. The colorbar for a denotes the hpf (hours post fertilization). The colorbar of b represents 1-(0–3 days), 2- (6–9 days), 3- (12–15 days), 4- (18–21 days) and 5- (24–27 days)). Pearson coefficient between the pseudotime estimated by monocle from the imputed data and the data labels for all the methods are shown for zebrafish development data (left), and EB differentiation data (right) in c. Source data are provided as a Source Data file.
