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Fig. 4 | Genome Biology

Fig. 4

From: SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Fig. 4

SLICER applied to cells from the developing mouse lung. a Cellular trajectory inferred by SLICER. The shape of each point indicates the time point (note that this information is used only after the fact for assessing whether the trajectory makes sense, not for constructing it). Color corresponds to inferred geodesic distance from the start cell (“differentiation progress”). The lines indicate edges used in the shortest paths to each point. Panels b through d show the expression levels of marker genes in each cell, with the cells ordered by developmental time. Panel b shows a marker for alveolar type 1 cells, c is an alveolar type 2 marker, and d is a marker for early progenitor cells. e Geodesic entropy plot for the trajectory shown in panel a. The dotted line represents an entropy value of 1, the threshold for branch detection. f Cells colored according to the branches that SLICER assigned using geodesic entropy. Note that no annotations were used in assigning cells to branches; instead, the interpretations indicated in the legend (AT1, AT2, or EP) were deduced based on marker genes such as those shown in panels bd after branch assignment

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