generate_tiles: generate tiles

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

generate tiles

Description

generate pixel tiles from punctual spatial assay coordinates

Usage

generate_tiles(
  vesalius_assay,
  tensor_resolution = 1,
  filter_grid = 0.01,
  filter_threshold = 0.995,
  verbose = TRUE
)

Arguments

vesalius_assay	a vesalius_assay object
tensor_resolution	numeric (range 0 - 1) describing the compression ratio to be applied to the final image. Default = 1
filter_grid	numeric (range 0 - 1) size of the grid used when filtering outlier beads. Defined as a proportion of total image size. Default = 0.1
filter_threshold	numeric (range 0 -1) describing the quantile
verbose	logical describing if progress message should be outputed

Details

This function converts punctual coordinates into pixel tiles. The first step is to filter outlier beads. Essentially removing any bead that lies outside of the main assay (seed filter_grid). If reqested the resolution of the image can be reduced by redudcing the relative distance between each coordinate pair (see reduce_tensor_resolution). Note that if the resolution is reduce all spatial indices are retained and counts will be merged together (see adjust_counts).

To create tiles, each coordinates is expanded by using Voronoi tesselation and each tile is raterised i.e "filled with pixel" (see rasterise). Prior to rasterisation, we remove all tiles that are above an area threshold. These tiles are artefacts of the tesselation algortihm that creates a "box" around all points and uses this as a boudary to generate each tile. They can also be generate by stray beads or holes in the data.

Value

a data.frame containing barcodes, x and you coordinates of each pixel as well as the original x/y coordinates

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.