Load annotations from a CSV file

Takes a character vector with paths to CSV files and returns a data.frame. The resulting data.frame can be added to a Seurat object using the AddMetaData function.

Usage

LoadAnnotationCSV(paths)

Arguments

paths

A character vector with paths to CSV files

Value

A data.frame object with barcode IDs and annotations

Details

NB: The files need to be loaded in the correct order. For example, if you have an object with 5 tissue sections, you should provide 5 paths in the correct order.

See also

Other pre-process: CreateMultiModalObject(), LoadAndMergeMatrices(), LoadImageInfo(), LoadImages(), LoadScaleFactors(), LoadSpatialCoordinates(), ReadVisiumData(), UpdateImageInfo()

Examples

library(semla)

se_mcolon <- readRDS(system.file("extdata/mousecolon", "se_mcolon", package = "semla"))
se_merged <- MergeSTData(se_mcolon, y = list(se_mcolon, se_mcolon))

# Get annotation file(s)
annotation_files <- system.file("extdata/mousecolon", 
                                "galt_spots.csv", 
                                package = "semla") |> rep(3)

# Load annotations
annotations <- LoadAnnotationCSV(annotation_files)
head(annotations)
#>                     selection
#> AAACACCAATAACTGC-1 background
#> AAACAGAGCGACTCCT-1 background
#> AAACAGCTTTCAGAAG-1 background
#> AAACAGGGTCTATATT-1 background
#> AAACCGGGTAGGTACC-1 background
#> AAACCGTTCGTCCAGG-1 background

# Edit data.frame if needed
annotations <- annotations |> 
  rename(test = selection)

# Add annotations to meta data
se_merged <- AddMetaData(se_merged, metadata = annotations)

# Plot new categorical variable
MapLabels(se_merged, column_name = "test")