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Set the cell plot node alpha scale

cell_node_scale_alpha.Rd

Defines the output alphas for a column mapped with cell_plot(alpha = ...). Numeric and integer columns are scaled continuously. Character and factor columns are treated as categorical levels.

Usage

cell_node_scale_alpha(object, alphas = c(0.2, 1), limits = NULL)

Arguments

object

A cell_plot recipe.

alphas

Values between zero and one. Supply two ordered values for a continuous or interpolated categorical range, or a named vector of per-level values when the mapped column is categorical.

limits

Optional scale limits for a ranged mapping. Supply two ordered numeric values. Named categorical alphas cannot be combined with limits.

Value

A modified cell_plot recipe.

Details

A length-2 alphas vector is an output range. build_cell_plot() normalizes continuous values, and interpolated categorical levels, to that interval. Rows with missing values in a mapped alpha column are dropped at build time with a warning. A named alphas vector assigns one opacity to each category, for example alphas = c(a = 0.2, b = 0.5, c = 1). Named values must cover every observed level and are not interpolated. limits belong to the ranged scale and cannot be combined with named alphas.

build_cell_plot() resolves alpha between zero and one. All renderers consume those resolved values directly.

This modifier requires an alpha mapping. One alpha shared by every point is set with cell_plot(alpha = <number>) instead.

See also

Other cell-plot-modifiers: cell_annotation(), cell_grid(), cell_illuminate(), cell_node_depth(), 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.
#> ℹ This message has been shown 60 times and will not be shown again this session.
#> ✔ 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")
#> 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, alpha = CD82) |>
  cell_node_scale_alpha(alphas = c(0.2, 1))


# One alpha per category
layout_data |>
  dplyr::mutate(group = dplyr::if_else(CD82 > median(CD82), "high", "low")) |>
  cell_plot(alpha = group) |>
  cell_node_scale_alpha(alphas = c(low = 0.3, high = 1))


# One alpha for every point
cell_plot(layout_data, alpha = 0.5)