R/graph.R

In zhixingfeng/rGDA: What the package does (short line)

ann_to_graph <- function(ann.data, min.prop = 0.5, min.len.prop = 0.5)
{
        gp <- make_empty_graph(nrow(ann.data))
        gp <- set_vertex_attr(gp, 'name', value = as.character(1:nrow(ann.data)))
        for (i in 1:nrow(ann.data)){
                if (i %% 100 == 0)
                        print(i)
                for (j in 1:nrow(ann.data)){
                        if (i == j) next
                        if (ann.data$start[j] < ann.data$start[i] | ann.data$start[j] >= ann.data$end[i] | ann.data$end[j] <= ann.data$end[i])
                                next

                        overlap.start <- max(ann.data$start[i], ann.data$start[j])
                        overlap.end <- min(ann.data$end[i], ann.data$end[j])
                        overlap.len <- overlap.end - overlap.start + 1

                        if (overlap.len < (ann.data$end[i] - ann.data$start[i] + 1) * min.len.prop )
                                next

                        cons_seq.i <- ann.data$cons_seq[[i]][ ann.data$cons_seq[[i]]>=4*overlap.start & ann.data$cons_seq[[i]]<=4*overlap.end+3 ]
                        cons_seq.j <- ann.data$cons_seq[[j]][ ann.data$cons_seq[[j]]>=4*overlap.start & ann.data$cons_seq[[j]]<=4*overlap.end+3 ]

                        n.overlap <- length(intersect(cons_seq.i, cons_seq.j))
		        
			if (n.overlap < min.prop*length(ann.data$cons_seq[[i]]) | n.overlap < min.prop*length(cons_seq.j))
				next

                        diff.loci.i <- floor(setdiff(cons_seq.i,cons_seq.j)/4)
                        diff.loci.j <- floor(setdiff(cons_seq.j,cons_seq.i)/4)

                        n.diff.loci.i <- length(intersect(diff.loci.i, ann.data$tested_loci[[j]]))
                        n.diff.loci.j <- length(intersect(diff.loci.j, ann.data$tested_loci[[i]]))

                        if (n.diff.loci.i > 0 | n.diff.loci.j > 0)
                                next
                        gp <- add_edges(gp, c(i,j))
                }
        }
        gp
}


ann_to_graph.legacy <- function(ann.data, min.prop = 0.5, min.len.prop = 0.5)
{
	gp <- make_empty_graph(nrow(ann.data))
	gp <- set_vertex_attr(gp, 'name', value = as.character(1:nrow(ann.data)))
	for (i in 1:nrow(ann.data)){
		if (i %% 100 == 0)
			print(i)
		for (j in 1:nrow(ann.data)){
			if (i == j) next
			if (ann.data$start[j] < ann.data$start[i] | ann.data$start[j] > ann.data$end[i] | ann.data$end[j] < ann.data$end[i])
				next
				
			overlap.start <- max(ann.data$start[i], ann.data$start[j])
			overlap.end <- min(ann.data$end[i], ann.data$end[j])
			overlap.len <- overlap.end - overlap.start + 1

			if (overlap.len < (ann.data$end[i] - ann.data$start[i] + 1) * min.len.prop )
				next

			cons_seq.i <- ann.data$cons_seq[[i]][ ann.data$cons_seq[[i]]>=4*overlap.start & ann.data$cons_seq[[i]]<=4*overlap.end+3 ]
			cons_seq.j <- ann.data$cons_seq[[j]][ ann.data$cons_seq[[j]]>=4*overlap.start & ann.data$cons_seq[[j]]<=4*overlap.end+3 ]

			n.overlap <- length(intersect(cons_seq.i, cons_seq.j))
			if (n.overlap < min.prop*length(cons_seq.i) | n.overlap < min.prop*length(cons_seq.j)) 
				next
			
			diff.loci.i <- floor(setdiff(cons_seq.i,cons_seq.j)/4)
			diff.loci.j <- floor(setdiff(cons_seq.j,cons_seq.i)/4)
		
			n.diff.loci.i <- length(intersect(diff.loci.i, ann.data$tested_loci[[j]]))
			n.diff.loci.j <- length(intersect(diff.loci.j, ann.data$tested_loci[[i]]))  
			
			if (n.diff.loci.i > 0 | n.diff.loci.j > 0)
				next
			gp <- add_edges(gp, c(i,j))	
		}
	}
	gp
}