This function adds spatial ecotype annotations to the metadata of single cells.
Arguments
- scmeta
Data frame containing single-cell metadata. Two columns (X and Y) for spatial coordinates are required.
- obj
A Seurat object returned from SpatialEcoTyper function.
- col
Character string specifying the name of the column in `obj@meta.data` containing the spatial ecotype annotations. Default is `"SE"`.
- dropcell
Logical. If TRUE, cells that cannot be assigned to any spatial ecotype (outside the radius) will be removed from the returned metadata. Default is TRUE.
Examples
library(data.table)
#>
#> Attaching package: ‘data.table’
#> The following objects are masked from ‘package:dplyr’:
#>
#> between, first, last
library(Seurat)
library(SpatialEcoTyper)
library(googledrive)
drive_deauth() # no Google sign-in is required
## Download a single-cell meta data
drive_download(as_id("1CgUOQKrWY_TG61o5aw7J9LZzE20D6NuI"),
"HumanMelanomaPatient1_subset_scmeta.tsv",
overwrite = TRUE)
#> File downloaded:
#> • HumanMelanomaPatient1_subset_scmeta.tsv
#> <id: 1CgUOQKrWY_TG61o5aw7J9LZzE20D6NuI>
#> Saved locally as:
#> • HumanMelanomaPatient1_subset_scmeta.tsv
## Obtain a Seurat object from SpatialEcoTyper result
drive_download(as_id("1nSPj2zRywFUdbo1fwiz77ds4NuM6bmV2"),
"Melanoma1_subset_SpatialEcoTyper_results.rds", overwrite = TRUE)
#> Error in map(as_id(id), get_one_file_id): ℹ In index: 1.
#> Caused by error in `.f()`:
#> ! Client error: (404) Not Found
#> File not found: 1nSPj2zRywFUdbo1fwiz77ds4NuM6bmV2.
#> • message: File not found: 1nSPj2zRywFUdbo1fwiz77ds4NuM6bmV2.
#> • domain: global
#> • reason: notFound
#> • location: fileId
#> • locationType: parameter
scmeta <- read.table("HumanMelanomaPatient1_subset_scmeta.tsv",
sep = "\t", header = TRUE, row.names = 1)
head(scmeta)
#> X Y CellType CellTypeName
#> HumanMelanomaPatient1__cell_3655 1894.706 -6367.766 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3657 1942.480 -6369.602 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3658 1963.007 -6374.026 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3660 1981.600 -6372.266 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3661 1742.939 -6374.851 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3663 1921.683 -6383.309 Fibroblast Fibroblasts
#> Region Dist2Interface
#> HumanMelanomaPatient1__cell_3655 Stroma -883.1752
#> HumanMelanomaPatient1__cell_3657 Stroma -894.8463
#> HumanMelanomaPatient1__cell_3658 Stroma -904.1115
#> HumanMelanomaPatient1__cell_3660 Stroma -907.8909
#> HumanMelanomaPatient1__cell_3661 Stroma -874.2712
#> HumanMelanomaPatient1__cell_3663 Stroma -903.6559
obj <- readRDS("Melanoma1_subset_SpatialEcoTyper_results.rds")$obj
## Transfer SE annotations to single cells
scmeta <- AnnotateCells(scmeta = scmeta, obj = obj, dropcell = TRUE)
head(scmeta)
#> X Y CellType CellTypeName
#> HumanMelanomaPatient1__cell_3655 1894.706 -6367.766 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3657 1942.480 -6369.602 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3658 1963.007 -6374.026 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3660 1981.600 -6372.266 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3661 1742.939 -6374.851 Fibroblast Fibroblasts
#> HumanMelanomaPatient1__cell_3663 1921.683 -6383.309 Fibroblast Fibroblasts
#> Region Dist2Interface SE
#> HumanMelanomaPatient1__cell_3655 Stroma -883.1752 SE0
#> HumanMelanomaPatient1__cell_3657 Stroma -894.8463 SE6
#> HumanMelanomaPatient1__cell_3658 Stroma -904.1115 SE6
#> HumanMelanomaPatient1__cell_3660 Stroma -907.8909 SE6
#> HumanMelanomaPatient1__cell_3661 Stroma -874.2712 SE0
#> HumanMelanomaPatient1__cell_3663 Stroma -903.6559 SE0