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Generate mesh data structure from coordinates, for input to DMT analysis

Source: R/utils_initdata.R
init_data.Rd

Creates a mesh from point coordinates using Delauney triangulation. Stores the points, triangles, and edges for the mesh, as well as a mapping from each triangle to its associated vertices. A gene-by-cell matrix can also be included, as well as additional metadata for each point.

Usage

init_data(X, Y, counts, meta_data = NULL, meta_vars_include = c())

Arguments

X, Y

A pair of numeric vectors with the coordinates for each of V points.

counts

A G x V gene-by-cell matrix of transcript counts.

meta_data

A data frame with additional cell metadata to include.

meta_vars_include

Names of columns in meta_data to include.

Value

A list containing the mesh data structures:

  • pts is a V-by-M data table with columns X and Y containing the coordinates of cells and additional metadata.

  • tris is a F-by-4 data table containing the X,Y coordinates of each triangle's centroid in the first two columns, and area and largest height of each triangle in the last two columns.

  • edges is a E-by-14 data table with columns from_pt, to_pt, from_tri, to_tri, x0_pt, x1_pt, y0_pt, y1_pt, x0_tri, x1_tri, y0_tri, y1_tri, length_pt, length_tri. If only one triangle uses an edge, then the from_tri, x0_tri, and y0_tri fields will contain NaN values.

  • tri_to_pt is a F-by-V sparse matrix with value 1 at (i,j) if triangle i uses point j as a vertex.

  • counts is a G x V gene-by-cell matrix of transcript counts.

Note that all indices stored in these data structures are 1-indexed.