Get and Set Additional Tool Data — Tool • SeuratObject

Use Tool to get tool data. If no additional arguments are provided, will return a vector with the names of tools in the object.

Tool(object, ...)

Tool(object, ...) <- value

# S3 method for Seurat
Tool(object, slot = NULL, ...)

# S3 method for Seurat
Tool(object, ...) <- value

Arguments

object: An object
...: Arguments passed to other methods
value: Information to be added to tool list
slot: Name of tool to pull

Value

If no additional arguments, returns the names of the tools in the object; otherwise returns the data placed by the tool requested

Note

For developers: set tool data using Tool<-. Tool<- will automatically set the name of the tool to the function that called Tool<-, so each function gets one entry in the tools list and cannot overwrite another function's entry. The automatic naming will also remove any method identifiers (eg. RunPCA.Seurat will become RunPCA); please plan accordingly

Examples

# Example function that adds unstructured data to tools
MyTool <- function(object) {
  sample.tool.output <- matrix(rnorm(n = 16), nrow = 4)
  # Note: `Tool<-` must be called from within a function
  # and the name of the tool will be generated from the function name
  Tool(object) <- sample.tool.output
  return(object)
}

# Run our tool
set.seed(42L)
pbmc_small <- MyTool(pbmc_small)

# Get a list of tools run
Tool(pbmc_small)
#> [1] "MyTool"

# Access specific tool data
Tool(pbmc_small, slot = "MyTool")
#>            [,1]        [,2]       [,3]       [,4]
#> [1,]  1.3709584  0.40426832  2.0184237 -1.3888607
#> [2,] -0.5646982 -0.10612452 -0.0627141 -0.2787888
#> [3,]  0.3631284  1.51152200  1.3048697 -0.1333213
#> [4,]  0.6328626 -0.09465904  2.2866454  0.6359504