R/tree2igraph.R

In bicbioeng/ctgPHYL: Package for Single-cell Data Visualization and Analysis

#' A Function to Convert Cell Relationships in a SIF object to igraph Format
#'
#' This function converts cell relationships in a cell tree into igraph format
#' @param relationships character vector of a cell tree in SIF format
#' @return a cell tree in igraph format
#' @importFrom igraph make_empty_graph add_edges set_edge_attr set_vertex_attr %>%
#' @keywords internal

tree2igraph <- function(relationships) {
    # turn the lines into a matrix of relationships with columns 1 and 3 being
    # related items and column 2 being the relationship type
    relationshipsMatrix <-
        matrix(unlist(strsplit(relationships, "\t")),
                ncol = 3, byrow = TRUE)
    # extract the relationship types from the matrix
    relationshipTypes <- relationshipsMatrix[, -c(1, 3)]
    # extract the related items into a vector by row
    relatedItems <- as.vector(t(relationshipsMatrix[, -2]))
    # get the unique items from related items to get the indices
    vertexIDs <- unique(relatedItems)
    # identify the related items by number instead of name
    relatedIDs <- vector(mode = "integer")
    for (i in seq_len(length(relatedItems))) {
        relatedIDs <-
            append(relatedIDs, which(vertexIDs %in% relatedItems[i]))
    }
    # make the igraph from the matrix
    cellIgraph <- make_empty_graph(n = length(vertexIDs)) %>%
        add_edges(relatedIDs)  %>%
        set_edge_attr("label", value = relationshipTypes) %>%
        set_vertex_attr("name", value = vertexIDs)
    cellIgraph
}