Figure 2. Force-Directed Layout of MEF Reprogramming SPADE Clusters.
(A–G) Schematic of the SPADE algorithm and modified FLOW-MAP layout. A 2D synthetic example data set (A) is first downsampled to a uniform density in ndimensional space (B), clustered hierarchically, and then upsampled (C), after which the cell clusters are connected by a minimum spanning tree, shown with the true 2D coordinates (D) and minimum spanning tree-derived layout (E), or alternatively connected by a FLOW-MAP graph, shown with the true 2D coordinates (F) and FLOW-MAP-derived layout (G). Two clusters that are close in 2D space, far apart on the minimum spanning tree layout and correctly placed adjacent to one another with the FLOW-MAP layout are indicated by purple arrows.
(H) Combined FLOW-MAP analysis of the full time course data sets for the Oct4-GFP, Nanog-GFP, and Nanog-Neo reprogramming systems. Hierarchical clustering was performed on each sample/time point individually using the following markers: PDGFRα, CD24, CD44, CD54, CD73, EpCAM, H3K9ac, Ki67, Klf4, Lin28, MEFSK4, Nanog, Oct4, SSEA1, Sox2, Thy1, and c-Myc to produce 500 clusters per sample. The cell clusters from each sample were then combined into a single FLOW-MAP graph layout and colored by cell system and time point as indicated.
(I–L) The FLOW-MAP layout from Figure 4H, colored to indicate the protein expression level of the specified markers: (I) Thy1, (J) SSEA1, (K) Lin28, and (L) Nanog.
See also Figure S2.