Adjust tissue coordinates for digital unrolling

This function takes a tbl_graph object as input generated with CutSpatialNetwork and attempts to calculate the unrolled tissue coordinates.

Usage

AdjustTissueCoordinates(full_graph, verbose = TRUE)

Arguments

full_graph

A tbl_graph object generated with CutSpatialNetwork

verbose

Print messages

Value

A tibble with "unrolled" tissue coordinates

Details

The algorithm is described briefly below:

First, the end point of the graph are identified. The outermost end point is assumed to be the starting point and the point at the center of the roll is assumed to be the end point.

Then, the algorithm tries to find the geodesic between the two end points, forming a band of nodes which represents the shortest path between the starting point and the end point.

The order of these shortest represents the distances along the x axis in the new coordinate system and the geodesics to all other nodes are used as distances on the y axis of the spots in the new coordinate system.

NB: The graph has to be fully connected. If multiple sub graphs are found, only the largest graph will be kept. It is crucial that edges has been cut properly with CutSpatialNetwork, otherwise the results will be inaccurate. See the package website for examples.