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Set the cell plot node depth scale

cell_node_depth.Rd

Tunes depth sizing for ggplot projections. Apparent point diameter scales with inverse camera distance so that a point twice as far from the camera is drawn at half the diameter. The point at mean depth keeps the constant node size from cell_plot(size = <number>) (or 1 when no constant is set).

Usage

cell_node_depth(object, focal_distance = 1.5)

Arguments

object

A cell_plot recipe.

focal_distance

Positive finite focal distance in the units of the mapped depth column. Defaults to 1.5.

Value

A modified cell_plot recipe.

Details

Depth sizing is on by default because depth is mapped to the z column. It is turned off with cell_plot(depth = NULL), which also makes this modifier an error. focal_distance controls the strength of the effect. Smaller values exaggerate size differences by depth; larger values flatten them.

Depth sizing scales one node size, so this modifier cannot be combined with cell_node_scale_size(). If a size column is mapped, depth sizing is ignored. cell_plot_interactive() ignores this modifier.

See also

cell_plot()

Other cell-plot-modifiers: cell_annotation(), cell_grid(), cell_illuminate(), cell_node_scale_alpha(), cell_node_scale_color(), cell_node_scale_size(), cell_theme()

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)

cell_plot(layout_data) |>
  cell_node_depth(focal_distance = 5)