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