rename pipeline function

Author: whtns

NAMESPACE

@@ -151,8 +151,8 @@ export(seurat_cluster)
 export(seurat_find_markers)
 export(seurat_integrate)
 export(seurat_integration_pipeline)
-export(seurat_pipeline)
 export(seurat_preprocess)
+export(seurat_process)
 export(seurat_reduce_dimensions)
 export(seurat_v5_integrate)
 export(seurat_v5_integration_pipeline)

R/docker_app.R

@@ -338,7 +338,7 @@ dockerSeuratApp <- function(object = panc8, loom_path = NULL, appTitle = NULL,
                         )
                         seu(reintegrated_seu)
                     } else {
-                        processed_seu <- seurat_pipeline(seu(), resolution = seq(0.2, 2, by = 0.2))
+                        processed_seu <- seurat_process(seu(), resolution = seq(0.2, 2, by = 0.2))
                         seu(processed_seu)
                     }
                     message("Complete!")
@@ -372,7 +372,7 @@ dockerSeuratApp <- function(object = panc8, loom_path = NULL, appTitle = NULL,
                         )
                         seu(reintegrated_seu)
                     } else {
-                        processed_seu <- seurat_pipeline(seu(), resolution = seq(0.2, 2, by = 0.2))
+                        processed_seu <- seurat_process(seu(), resolution = seq(0.2, 2, by = 0.2))
                         seu(processed_seu)
                     }
                     message("Complete!")

R/minimal_app.R

@@ -339,7 +339,7 @@ minimalSeuratApp <- function(object = panc8, loom_path = NULL, appTitle = NULL,
                         )
                         seu(reintegrated_seu)
                     } else {
-                        processed_seu <- seurat_pipeline(seu(), resolution = seq(0.2, 2, by = 0.2))
+                        processed_seu <- seurat_process(seu(), resolution = seq(0.2, 2, by = 0.2))
                         seu(processed_seu)
                     }
                     message("Complete!")
@@ -373,7 +373,7 @@ minimalSeuratApp <- function(object = panc8, loom_path = NULL, appTitle = NULL,
                         )
                         seu(reintegrated_seu)
                     } else {
-                        processed_seu <- seurat_pipeline(seu(), resolution = seq(0.2, 2, by = 0.2))
+                        processed_seu <- seurat_process(seu(), resolution = seq(0.2, 2, by = 0.2))
                         seu(processed_seu)
                     }
                     message("Complete!")

R/pipeline.R

@@ -142,16 +142,16 @@ seurat_v5_integration_pipeline <- function(seu, resolution = seq(0.2, 2.0, by =
 #' @param resolution Resolution for clustering cells. Default set to 0.6.
 #' @param reduction Dimensional reduction object seu
 #' @param organism Organism
-#' @param ... Extra parameters passed to seurat_pipeline
+#' @param ... Extra parameters passed to seurat_process
 #'
 #' @return
 #' @export
 #'
 #' @examples
 #'
-#' processed_seu <- seurat_pipeline(panc8)
+#' processed_seu <- seurat_process(panc8)
 #'
-seurat_pipeline <- function(seu, assay = "gene", resolution = 0.6, reduction = "pca", organism = "human", ...) {
+seurat_process <- function(seu, assay = "gene", resolution = 0.6, reduction = "pca", organism = "human", ...) {
     assays <- names(seu@assays)
 
     assays <- assays[assays %in% c("gene", "transcript")]

R/seurat_app.R

@@ -714,7 +714,7 @@ seuratApp <- function(preset_project, appTitle = "seuratTools", organism_type =
                         )
                         seu(reintegrated_seu)
                     } else {
-                        subset_seu <- seurat_pipeline(seu(), resolution = seq(0.2, 2, by = 0.2), legacy_settings = input$legacySettingsSubset) # markermarker
+                        subset_seu <- seurat_process(seu(), resolution = seq(0.2, 2, by = 0.2), legacy_settings = input$legacySettingsSubset) # markermarker
                         seu(subset_seu)
                     }
                     message("Complete!")
@@ -748,7 +748,7 @@ seuratApp <- function(preset_project, appTitle = "seuratTools", organism_type =
                         )
                         seu(reintegrated_seu)
                     } else {
-                        subset_seu <- seurat_pipeline(seu(),
+                        subset_seu <- seurat_process(seu(),
                             resolution = seq(0.2,
                                 2,
                                 by = 0.2

R/workflow.R

@@ -78,7 +78,7 @@ integration_workflow <- function(batches, excluded_cells = NULL, resolution = se
 #' clustered_human_seu <- clustering_workflow(panc8, experiment_name = "seurat_pancreas", organism = "human")
 #' clustered_mouse_seu <- clustering_workflow(baron2016singlecell)
 clustering_workflow <- function(seu, excluded_cells, resolution = seq(0.2, 2.0, by = 0.2), organism = "human", experiment_name = "default_experiment", ...) {
-    seu <- seurat_pipeline(seu, resolution = resolution, organism = organism, ...)
+    seu <- seurat_process(seu, resolution = resolution, organism = organism, ...)
 
     seu <- record_experiment_data(seu, experiment_name, organism)