Run Force-Directed Layout (Fruchterman-Reingold algorithm)

Usage

RunFR(object, ...)

# S3 method for class 'Seurat'
RunFR(
  object,
  reduction = NULL,
  dims = NULL,
  features = NULL,
  assay = NULL,
  layer = "data",
  graph = NULL,
  neighbor = NULL,
  k.param = 20,
  ndim = 2,
  niter = 500,
  reduction.name = "FR",
  reduction.key = "FR_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

# Default S3 method
RunFR(
  object,
  assay = NULL,
  ndim = 2,
  niter = 500,
  reduction.key = "FR_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

Arguments

object: An object. This can be a Seurat object, a Neighbor object, or a Graph object.
...: Passed to igraph::layout_with_fr.
reduction: Linear reduction used as input.
dims: Dimensions to use. Supply only one of dims, features, neighbor, or graph.
features: Features used instead of a reduction.
assay: Assay to use. NULL uses the default assay.
layer: Assay layer to use.
graph: Neighbor-graph edges.
neighbor: Neighbor object to be used.
k.param: The number of nearest neighbors to consider.
ndim: The number of dimensions for the force-directed layout.
niter: The number of iterations for the force-directed layout.
reduction.name: Reduction to be stored in the Seurat object.
reduction.key: The prefix for the column names of the force-directed layout embeddings.
verbose: Whether to print the message. Default is TRUE.
seed.use: Random seed.

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 05:00:23] Start standard processing workflow...
#> ℹ [2026-08-30 05:00:23] Checking a list of <Seurat>...
#> ! [2026-08-30 05:00:23] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 05:00:23] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 05:00:23] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 05:00:23] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 05:00:23] Number of available HVF: 2000
#> ℹ [2026-08-30 05:00:23] Finished check
#> ℹ [2026-08-30 05:00:23] Perform `ScaleData()`
#> ℹ [2026-08-30 05:00:23] Perform pca linear dimension reduction
#> ℹ [2026-08-30 05:00:24] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 05:00:24] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 05:00:24] Reorder clusters...
#> ℹ [2026-08-30 05:00:24] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 05:00:24] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 05:00:33] Standard processing workflow completed
pancreas_sub <- RunFR(
  object = pancreas_sub,
  graph = "Standardpca_SNN",
  niter = 100
)
#> ℹ [2026-08-30 05:00:33] Running force-directed layout
#> Warning: No assay specified, setting assay as RNA by default.
#> Warning: Adding a command log without an assay associated with it
#> ℹ [2026-08-30 05:00:33] Force-directed layout computed
CellDimPlot(
  pancreas_sub,
  group.by = "CellType",
  reduction = "fr"
)