Reorder idents by the gene expression

Usage

srt_reorder(
  object,
  features = NULL,
  reorder_by = NULL,
  layer = "data",
  assay = NULL,
  log = TRUE,
  distance_metric = "euclidean",
  verbose = TRUE,
  srt = NULL
)

Arguments

object: A Seurat object.
features: Features to plot: a character vector or a named list of assay gene names or numeric metadata columns.
reorder_by: Reorder groups instead of idents.
layer: Assay layer to use.
assay: Assay to use. NULL uses the default assay.
log: Whether log1p transformation needs to be applied.
distance_metric: Metric to compute distance.
verbose: Whether to print the message. Default is TRUE.
srt: Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-10-12 00:02:14] Start standard processing workflow...
#> ℹ [2026-10-12 00:02:14] Checking a list of <Seurat>...
#> ! [2026-10-12 00:02:14] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-10-12 00:02:14] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-10-12 00:02:14] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-10-12 00:02:14] Use the separate HVF from `srt_list`
#> ℹ [2026-10-12 00:02:14] Number of available HVF: 2000
#> ℹ [2026-10-12 00:02:15] Finished check
#> ℹ [2026-10-12 00:02:15] Perform `ScaleData()`
#> ℹ [2026-10-12 00:02:15] Perform pca linear dimension reduction
#> ℹ [2026-10-12 00:02:15] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-10-12 00:02:15] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-10-12 00:02:15] Reorder clusters...
#> ℹ [2026-10-12 00:02:16] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-10-12 00:02:16] Perform umap nonlinear dimension reduction
#> ✔ [2026-10-12 00:02:24] Standard processing workflow completed
pancreas_sub <- srt_reorder(
  pancreas_sub,
  reorder_by = "SubCellType",
  layer = "data"
)
#> ℹ [2026-10-12 00:02:24] Skip `log1p()` because `layer = data` is not "counts"