View source: R/Celltype_annotation_Seurat.R
Celltype_annotation_Seurat | R Documentation |
Uses "marker_list" from Seurat object for cell annotation
Celltype_annotation_Seurat(
seurat_obj,
gene_list,
species,
cluster_col = "seurat_clusters",
assay = "RNA",
save_path = NULL,
metric_names = NULL,
colour_low = "white",
colour_high = "navy",
colour_low_mertic = "white",
colour_high_mertic = "navy"
)
seurat_obj |
Enter the Seurat object with annotation columns such as "seurat_cluster" in meta.data to be annotated. |
gene_list |
Enter the standard "Marker_list" generated by the Seurat object database for the SlimR package, generated by the "read_seurat_markers()" function. |
species |
This parameter selects the species "Human" or "Mouse" for standard gene format correction of markers entered by "Marker_list". |
cluster_col |
Enter annotation columns such as "seurat_cluster" in meta.data of the Seurat object to be annotated. Default parameters use "cluster_col = 'seurat_clusters'". |
assay |
Enter the assay used by the Seurat object, such as "RNA". Default parameters use "assay = 'RNA'". |
save_path |
The output path of the cell annotation picture. Example parameters use "save_path = './SlimR/Celltype_annotation_Seurat/'". |
metric_names |
Change the row name for the input mertics, not recommended unless necessary. (NULL is used as default parameter) |
colour_low |
Color for lowest expression level. (default = "white") |
colour_high |
Color for highest expression level. (default = "black") |
colour_low_mertic |
Color for lowest mertic level. (default = "white") |
colour_high_mertic |
Color for highest mertic level. (default = "black") |
The cell annotation picture is saved in "save_path".
Other Other_Functions_Provided_By_SlimR:
Celltype_annotation_Cellmarker2()
,
Celltype_annotation_Excel()
,
Celltype_annotation_PanglaoDB()
## Not run:
Celltype_annotation_Seurat(seurat_obj = sce,
gene_list = Markers_list_Seurat,
species = "Human",
cluster_col = "seurat_clusters",
assay = "RNA",
save_path = file.path(tempdir(),"SlimR_Celltype_annotation_Seurat")
colour_low = "white",
colour_high = "navy",
colour_low_mertic = "white",
colour_high_mertic = "navy",
)
## End(Not run)
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