Fetch graph layout coordinates

Fetches a stored 3D layout from CellGraph objects and optionally joins node-level variables retrieved with FetchData.

Usage

FetchLayoutData(object, ...)

# S3 method for class 'CellGraph'
FetchLayoutData(
  object,
  layout_method = "wpmds_3d",
  vars = NULL,
  add_marker = FALSE,
  layer = NULL,
  ...
)

# S3 method for class 'CellGraphList'
FetchLayoutData(
  object,
  layout_method = "wpmds_3d",
  vars = NULL,
  cells = NULL,
  add_marker = FALSE,
  layer = NULL,
  ...
)

# S3 method for class 'PNAAssay'
FetchLayoutData(
  object,
  layout_method = "wpmds_3d",
  vars = NULL,
  cells = NULL,
  add_marker = FALSE,
  layer = NULL,
  ...
)

# S3 method for class 'PNAAssay5'
FetchLayoutData(
  object,
  layout_method = "wpmds_3d",
  vars = NULL,
  cells = NULL,
  add_marker = FALSE,
  layer = NULL,
  ...
)

# S3 method for class 'Seurat'
FetchLayoutData(
  object,
  layout_method = "wpmds_3d",
  vars = NULL,
  cells = NULL,
  assay = NULL,
  add_marker = FALSE,
  layer = NULL,
  ...
)

Arguments

object

An object

...

Additional parameters passed to other methods

layout_method

Name of a stored layout, typically one computed with ComputeLayout or loaded with LoadCellGraphs. Default is "wpmds_3d". The layout must contain x, y, and z coordinates.

vars

Optional character vector of node-level variables to fetch with FetchData (markers, metadata columns, graph vertex attributes, or reduction embeddings). A variable that is present on some cells and missing on others is filled with NA and a warning names those cells. A variable missing from every cell aborts.

add_marker

If TRUE, add a marker column with the marker label of each node. Labels are read from the counts matrix. Nodes with no count are NA.

layer

Name of a node matrix layer passed to FetchData. NULL (default) uses the same layer selection as FetchData.CellGraph. On a CellGraphList, a missing layer omits only that layer's features; metadata and other requested variables are still returned. Remaining names are not looked up in counts or other layers.

cells

Component IDs to fetch. If NULL, all loaded CellGraph objects are used. Unloaded graphs raise an error when they are included in cells.

assay

Name of assay to fetch layouts from

Value

A tbl_df with columns x, y, z and any requested vars. add_marker = TRUE also adds a marker column with the marker label of each node. Methods that extract from multiple components also include a component column.

Examples

library(pixelatorR)

se <- ReadPNA_Seurat(minimal_pna_pxl_file(), verbose = FALSE)
#> 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.
se <- LoadCellGraphs(se, cells = colnames(se)[1], add_layouts = TRUE, verbose = FALSE)
#> Warning: The `add_layouts` argument of `LoadCellGraphs()` is deprecated as of pixelatorR
#> 0.21.0.
#> ℹ The argument will be removed in a future release.
#> ℹ Layouts can be computed with `ComputeLayout()`.
#> ℹ The deprecated feature was likely used in the pixelatorR package.
#>   Please report the issue to the authors.
#> 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.
cg <- CellGraphs(se)[[1]]

# Coordinates only
layout <- FetchLayoutData(cg)

# Include marker counts
layout <- FetchLayoutData(cg, vars = "B2M")

# Include marker labels
layout <- FetchLayoutData(cg, add_marker = TRUE)

# Combine layouts from a CellGraphList
cgl <- CellGraphs(se)
layout <- FetchLayoutData(cgl, cells = colnames(se)[1], vars = "B2M")

# PNAAssay method
layout <- FetchLayoutData(se[["PNA"]], cells = colnames(se)[1], vars = "B2M")

# Seurat method
layout <- FetchLayoutData(se, cells = colnames(se)[1], vars = "B2M")