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Lineage weights from a trajectory graph

Source: R/paths_from_graph.R
paths_from_graph.Rd

paths_from_graph() gives the lineage weights of the cells of a trajectory graph, such as the principal graph of Monocle3 or a minimum spanning tree of clusters, for assign_paths(). Each lineage is the shortest path from the root node to an end node, and a cell is on it (weight 1) when its node is on that path.

Usage

paths_from_graph(cell_node, edges, root, endpoints = NULL)

Arguments

cell_node

A vector with the node of each cell, named by cell. The nodes are compared with the node names of edges as character strings.

edges

A matrix or data frame whose first two columns hold the two nodes of each edge of the graph, which is taken as undirected.

root

The name of the root node.

endpoints

The names of the end nodes, one lineage each; the default, NULL, takes every node with one edge other than the root, in the order in which they first appear in edges.

Value

A numeric matrix with one row per cell, in the order and with the names of cell_node, and one column per end node, named by it, holding 1 when the node of the cell is on the path from the root to that end node and 0 otherwise.

Details

The paths are found with igraph::shortest_paths() on the unweighted graph, so this function needs the suggested package igraph. In a tree, as principal graphs and minimum spanning trees are, the path from the root to each end node is the only one. Every node of cell_node must be a node of edges, and every end node must be reachable from the root.

References

Van den Berge K, Roux de Bézieux H, Street K, Saelens W, Cannoodt R, Saeys Y, Dudoit S, Clement L (2020). Trajectory-based differential expression analysis for single-cell sequencing data. Nature Communications 11, 1201. doi:10.1038/s41467-020-14766-3

Csárdi G, Nepusz T (2006). The igraph software package for complex network research. InterJournal Complex Systems, 1695. https://igraph.org

See also

assign_paths(), which turns these weights into path labels.

Other input helpers: as_scmp(), assign_paths(), create_scmp()

Author

Priyansh Srivastava spriyansh29@gmail.com

Examples

# A tree: the root R, a segment A-B shared by the end nodes C and D, and
# the end node E that branches off at A
edges <- rbind(
    c("R", "A"), c("A", "B"), c("B", "C"), c("B", "D"), c("A", "E")
)
cell_node <- c(
    cell1 = "R", cell2 = "A", cell3 = "B", cell4 = "C", cell5 = "D",
    cell6 = "E"
)
if (requireNamespace("igraph", quietly = TRUE)) {
    weights <- paths_from_graph(cell_node, edges, root = "R")
    print(weights)
    # With a pseudotime that every lineage shares
    assign_paths(c(0, 1, 2, 3, 3, 2), weights)
}
#>       C D E
#> cell1 1 1 1
#> cell2 1 1 1
#> cell3 1 1 0
#> cell4 1 0 0
#> cell5 0 1 0
#> cell6 0 0 1
#>       Pseudotime      Path
#> cell1          0      root
#> cell2          1      root
#> cell3          2 C_links_D
#> cell4          3         C
#> cell5          3         D
#> cell6          2         E