Nonlinear dimensionality reduction based visualization of single-cell RNA sequencing data

Journal of Analytical Science and Technology

Table 2 Mean and median PCC values obtained from the Mantel test for various DR techniques on all three scRNA-seq Datasets

scRNA-seq dataset	DR techniques	Mean PCC value	Median PCC value
Human pancreas	CP-PaCMAP	0.85	0.85
	PaCMAP	0.83	0.84
	UMAP	0.78	0.80
	t-SNE	0.80	0.82
	TRIMAP	0.76	0.76
	PHATE	0.75	0.74
	IVIS	0.72	0.73
Human skeletal muscle	CP-PaCMAP	0.80	0.79
	PaCMAP	0.77	0.76
	UMAP	0.77	0.77
	t-SNE	0.76	0.77
	TRIMAP	0.74	0.75
	PHATE	0.73	0.74
	IVIS	0.76	0.77
Human heart	CP-PaCMAP	0.77	0.78
	PaCMAP	0.75	0.76
	UMAP	0.74	0.76
	t-SNE	0.73	0.74
	TRIMAP	0.73	0.72
	PHATE	0.72	0.73
	IVIS	0.70	0.72