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Add rotating coordinates to a cell plot

cell_coord_rotate.Rd

Records rotation geometry for an animation renderer. This sets a rotation sequence rather than a single static view. The number of frames, and whether the animation returns through them, belong to cell_plot_animate(), not this modifier. Printed ggplot and Plotly views keep the unrotated coordinates. The default axis is "y", which spins the cell left to right on screen.

Usage

cell_coord_rotate(
  object,
  axis = "y",
  max_degree = 360,
  origin = c("origo", "centroid")
)

Arguments

object

A cell_plot recipe.

axis

Axis around which coordinates are rotated. Use "x", "y", or "z" for a principal axis, or three finite numeric values for an arbitrary axis. Numeric axes are normalized before they are stored.

max_degree

Maximum rotation angle from -360 to 360 degrees. Positive angles follow the right-hand rule; use a negative angle to reverse direction.

origin

Rotation origin. "origo" uses (0, 0, 0). "centroid" calculates the centroid independently within each cell_grid() panel.

Value

A modified cell_plot recipe.

See also

cell_plot_animate(), cell_illuminate()

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_coord_rotate(axis = "y")