Create S4 spatLocsObj — createSpatLocsObj • GiottoClass

Create an S4 spatLocsObj

Usage

createSpatLocsObj(
  coordinates,
  name = "test",
  spat_unit = "cell",
  provenance = NULL,
  misc = NULL,
  numeric_format = c("pair", "triplet"),
  verbose = TRUE,
  ...
)

Arguments

coordinates: spatial coordinates
name: name of spatLocsObj
spat_unit: spatial unit of aggregated expression (e.g. 'cell')
provenance: origin data of aggregated expression information (if applicable)
misc: misc
numeric_format: character. One of "pair" (default) or "triplet". Whether numeric inputs should be understood as XY pairs or XYZ triplets.
verbose: verbosity
...: additional params to pass

Value

spatLocsObj

Examples

# from data.frame
x <- data.frame(
    cell_ID = c("cell_1", "cell_2", "cell_3"),
    sdimx = c(6637.881, 6471.978, 6801.610),
    sdimy = c(-5140.465, -4883.541, -4968.685)
)
s1 <- createSpatLocsObj(coordinates = x, name = "raw")
#> There are non numeric or integer columns for the spatial location
#>  input at column position(s): 1
#>  The first non-numeric column will be considered as a cell ID
#>  to test for consistency with the expression matrix
#>  Other non numeric columns will be removed
plot(s1)


# from matrix
m <- matrix(c(2 ,3, 4, 2), ncol = 2)
rownames(m) <- c("cell1", "cell2")
s2 <- createSpatLocsObj(m)
#> [spatlocs] matrix input has rownames.
#>  Using these as IDs.
#> There are non numeric or integer columns for the spatial location
#>  input at column position(s): 3
#>  The first non-numeric column will be considered as a cell ID
#>  to test for consistency with the expression matrix
#>  Other non numeric columns will be removed
plot(s2)


# from numeric xy pairs
num2d <- c(1, 3, 5, 9)
s3 <- createSpatLocsObj(num2d)
plot(s3)

# from numeric xyz triplets
num3d <- c(3, 2, 9, 3, 8, 5)
s4 <- createSpatLocsObj(num3d, numeric_format = "triplet")
plot(s4)