Validate a table column map

Creates a validated description of how a generic delimited table maps to the cellspec columns. Source names are checked for shape here and checked against the input table by cs_read().

Usage

cs_column_map(
  cell_id,
  x,
  y,
  image_id = NULL,
  sample_id = NULL,
  area = NULL,
  coordinate_unit = c("um", "px"),
  measurements = NULL
)

Arguments

cell_id

Source column containing the cell identifier.

x

Source column containing the x coordinate.

y

Source column containing the y coordinate.

image_id

Optional source column containing image identifiers.

sample_id

Optional source column containing sample identifiers.

area

Optional source column containing positive cell areas.

coordinate_unit

Coordinate unit for x and y: micrometres or pixels.

measurements

Optional data frame with source_name, kind, marker, compartment, statistic and unit metadata columns. Measurements of kind other get other: identifiers as described for keep_other in cs_read().

Value

An object of class cs_column_map, a named list with the mapped source names, coordinate unit and validated measurement metadata.

See also

cs_read()

Other adapters: cs_detect_format(), cs_formats(), cs_read()

Examples

cs_column_map(
  "Cell ID", "Centroid X", "Centroid Y",
  measurements = data.frame(
    source_name = "CD3e Mean", kind = "intensity", marker = "CD3e",
    compartment = "cell", statistic = "mean", unit = "a.u."
  )
)
#> $cell_id
#> [1] "Cell ID"
#> 
#> $x
#> [1] "Centroid X"
#> 
#> $y
#> [1] "Centroid Y"
#> 
#> $image_id
#> NULL
#> 
#> $sample_id
#> NULL
#> 
#> $area
#> NULL
#> 
#> $coordinate_unit
#> [1] "um"
#> 
#> $measurements
#>   source_name      kind marker compartment statistic unit
#> 1   CD3e Mean intensity   CD3e        cell      mean a.u.
#> 
#> attr(,"class")
#> [1] "cs_column_map" "list"