Compute a graph layout

Computes graph layouts for component graphs.

Usage

ComputeLayout(object, ...)

# S3 method for class 'tbl_graph'
ComputeLayout(
  object,
  layout_method = c("cpmds", "pmds", "wpmds"),
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  ...
)

# S3 method for class 'CellGraph'
ComputeLayout(
  object,
  layout_method = c("cpmds", "pmds", "wpmds"),
  layout_name = NULL,
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  ...
)

# S3 method for class 'MPXAssay'
ComputeLayout(
  object,
  layout_method = c("cpmds", "pmds", "wpmds"),
  layout_name = NULL,
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  verbose = TRUE,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  cl = NULL,
  ...
)

# S3 method for class 'CellGraphAssay'
ComputeLayout(
  object,
  layout_method = c("cpmds", "pmds", "wpmds"),
  layout_name = NULL,
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  verbose = TRUE,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  cl = NULL,
  ...
)

# S3 method for class 'CellGraphAssay5'
ComputeLayout(
  object,
  layout_method = c("cpmds", "pmds", "wpmds"),
  layout_name = NULL,
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  verbose = TRUE,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  cl = NULL,
  ...
)

# S3 method for class 'PNAAssay'
ComputeLayout(
  object,
  layout_method = c("cpmds", "pmds", "wpmds"),
  layout_name = NULL,
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  verbose = TRUE,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  cl = NULL,
  ...
)

# S3 method for class 'PNAAssay5'
ComputeLayout(
  object,
  layout_method = c("cpmds", "pmds", "wpmds"),
  layout_name = NULL,
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  verbose = TRUE,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  cl = NULL,
  ...
)

# S3 method for class 'Seurat'
ComputeLayout(
  object,
  assay = NULL,
  layout_method = c("cpmds", "pmds", "wpmds"),
  layout_name = NULL,
  dim = 3,
  normalize_layout = FALSE,
  project_on_unit_sphere = FALSE,
  pivots = 100,
  seed = 123,
  verbose = TRUE,
  custom_layout_function = NULL,
  custom_layout_function_args = NULL,
  cl = NULL,
  ...
)

Arguments

object: An object
...: Additional parameters passed to other methods
layout_method: The method for calculating the graph layout: coarsened Pivot MDS (cpmds), weighted Pivot MDS ("wpmds") or Pivot MDS (pmds)
dim: An integer specifying the dimensions of the layout (2 or 3). Note that for "cpmds", "pmds" and "wpmds", the x and y coordinates will be identical regardless if dim is set to 2 or 3.
normalize_layout: Logical specifying whether the coordinate system should be centered at origo and the coordinates scaled such that their median length (euclidean norm) is 1.
project_on_unit_sphere: Should the resulting layout be projected onto a unit sphere?
pivots: Used for Pivot MDS layout algorithms. See ?layout_with_pmds for details
seed: Set seed for reproducibility
custom_layout_function: A custom function for layout computation. The function should take a tbl_graph object and a dim value as input and return a matrix of dimensions NxD, where N is the number of nodes and D is equal to dim. Note that this will override the layout_method.
custom_layout_function_args: A list of arguments passed to custom_layout_function. The dim is automatically passed to custom_layout_function and should not be included in custom_layout_function_args.
layout_name: The name of the computed layout. If this name is not given, the layout_method will be used as the name. If dim = 3, a suffix of "_3d" will be added to the layout name. This behavior is ignored if layout_name is provided.
verbose: Print messages
cl: An integer to indicate number of child-processes (integer values are ignored on Windows) for parallel evaluations. See Details on performance in the documentation for pbapply. The default is NULL, which means that no parallelization is used.
assay: Name of assay to compute layouts for

Value

An object containing a graph layout

Examples

library(pixelatorR)
library(dplyr)

pxl_file <- minimal_pna_pxl_file()

# Load example data
seur <- ReadPNA_Seurat(pxl_file)
#> ✔ Created a <Seurat> object with 5 cells and 158 targeted surface proteins

# Load 1 cellgraph
seur <- LoadCellGraphs(seur,
  cells = colnames(seur)[4],
  force = TRUE
)
#> ℹ Fetching edgelists for 1 cells 
#> → Creating <CellGraph> objects
#> → Fetching marker counts
#> → Adding marker counts to <CellGraph> object(s)
#> ✔ Successfully loaded 1 <CellGraph> object(s).

# Get CellGraph
cg <- CellGraphs(seur)[[colnames(seur)[4]]]

# Get tbl_graph object
tbl_graph <- slot(cg, name = "cellgraph")

# Compute layout for a tbl_graph
layout <- ComputeLayout(tbl_graph, layout_method = "cpmds")

# Visualize
plotly::plot_ly(
  data = layout, x = ~x, y = ~y, z = ~z,
  type = "scatter3d", mode = "markers", marker = list(size = 2)
)



# Compute layout for a CellGraph
cg <- ComputeLayout(cg, layout_method = "cpmds")


# Compute layout for a PNAAssay
cg_assay <- ComputeLayout(seur[["PNA"]], layout_method = "cpmds")
#> ℹ Computing layouts for 1 graphs

# Seurat method
seur <- ComputeLayout(seur)
#> ℹ Computing layouts for 1 graphs

# Visualize with Plot3DGraph
Plot3DGraph(seur, cell_id = colnames(seur)[4], layout_method = "cpmds_3d")

Usage

Arguments

Value

See also

Examples