Reorder idents by the gene expression

Usage

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

Arguments

srt: A Seurat object.
features: A character vector or a named list of features to plot. Features can be gene names in Assay or names of numeric columns in meta.data.
reorder_by: Reorder groups instead of idents.
layer: Which layer to use. Default is data.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
log: Whether log1p transformation needs to be applied. Default is TRUE.
distance_metric: Metric to compute distance. Default is "euclidean".
verbose: Whether to print the message. Default is TRUE.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2026-04-26 02:39:04] Start standard processing workflow...
#> ℹ [2026-04-26 02:39:05] Checking a list of <Seurat>...
#> ! [2026-04-26 02:39:05] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-04-26 02:39:05] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-04-26 02:39:08] Perform `Seurat::FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-04-26 02:39:08] Use the separate HVF from `srt_list`
#> ℹ [2026-04-26 02:39:09] Number of available HVF: 2000
#> ℹ [2026-04-26 02:39:09] Finished check
#> ℹ [2026-04-26 02:39:09] Perform `Seurat::ScaleData()`
#> ℹ [2026-04-26 02:39:09] Perform pca linear dimension reduction
#> ℹ [2026-04-26 02:39:10] Use stored estimated dimensions 1:20 for Standardpca
#> ℹ [2026-04-26 02:39:10] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-04-26 02:39:10] Reorder clusters...
#> ℹ [2026-04-26 02:39:11] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-04-26 02:39:11] Perform umap nonlinear dimension reduction
#> ℹ [2026-04-26 02:39:11] Perform umap nonlinear dimension reduction using Standardpca (1:20)
#> ℹ [2026-04-26 02:39:16] Perform umap nonlinear dimension reduction using Standardpca (1:20)
#> ✔ [2026-04-26 02:39:22] Standard processing workflow completed
pancreas_sub <- srt_reorder(
  pancreas_sub,
  reorder_by = "SubCellType",
  layer = "data"
)
#> ℹ [2026-04-26 02:39:23] Skip `log1p()` because `layer = data` is not "counts"