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Build a cell plot recipe

build_cell_plot.Rd

Resolves mappings, constants, scales, illumination, and display defaults without drawing a plot. The returned object has the same top-level fields as the input recipe, with data ordered by the arrange mapping. Rows with missing values (NA) in mapped size or alpha columns are removed with a warning before color illumination is calculated. Color, size, and alpha resolve to one value each when the aesthetic is constant or unmapped. Named categorical size and alpha scales assign one resolved value per level. Illumination is calculated after color-scale training and stored separately from the unilluminated resolved colors used by legends. Other projection-specific transformations, such as apparent size from depth, are applied by renderers rather than during the build.

Usage

build_cell_plot(object)

Arguments

object

A cell_plot recipe.

Value

A cell_plot_built object containing resolved plot data and rendering instructions.

Examples

se <- ReadPNA_Seurat(minimal_pna_pxl_file())
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmp3BjCtL/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> ✔ Created a <Seurat> object with 5 cells and 158 targeted surface proteins
se <- LoadCellGraphs(se, cells = colnames(se)[4], verbose = FALSE) |>
  ComputeLayout(layout_method = "spectral")
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmp3BjCtL/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> ℹ Computing layouts for 1 graphs

cell_graph <- CellGraphs(se)[[4]]

layout_data <- FetchLayoutData(cell_graph, vars = "CD82", layout_method = "spectral_3d") |>
  # Downsample to speed up tests
  dplyr::slice_sample(n = 5000)

built <- cell_plot(layout_data, color = "CD82") |>
  build_cell_plot()