df2sf: From ordinary data frame to sf to construct SFE object

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

From ordinary data frame to sf to construct SFE object

Description

While the SpatialFeatureExperiment constructor and *Geometry replacement methods can convert properly formatted ordinary data frames into sf objects which are used to store the geometries internally, the user might want to do the conversion, check if the geometry is valid, and inspect and fix any invalid geometries.

Usage

df2sf(
  df,
  spatialCoordsNames = c("x", "y"),
  spotDiameter = NA,
  geometryType = c("POINT", "LINESTRING", "POLYGON", "MULTIPOINT", "MULTILINESTRING",
    "MULTIPOLYGON"),
  group_col = "group",
  id_col = "ID",
  subid_col = "subID",
  check = TRUE,
  BPPARAM = deprecated(),
  ...
)

Arguments

df	An ordinary data frame, i.e. not sf. Or a matrix that can be converted to a data frame.
spatialCoordsNames	Column names in df that specify spatial coordinates.
spotDiameter	Spot diameter for technologies with arrays of spots of fixed diameter per slide, such as Visium, ST, DBiT-seq, and slide-seq. The diameter must be in the same unit as the coordinates in the *Geometry arguments. Ignored for geometries that are not POINT or MULTIPOINT.
geometryType	Type of geometry to convert the ordinary data frame to. If the geometry in df is de facto points, then this argument will be ignored and the returned sf will have geometry type POINT.
group_col	Column to indicate which coordinates for which MULTI geometry, such as to identify which MULTIPOLYGON or MULTIPOINT.
id_col	Column to indicate coordinates for which geometry, within a MULTI geometry if applicable, such as to identify which POLYGON or which polygon within a MULTIPOLYGON.
subid_col	Column to indicate coordinates for holes in polygons.
check	Logical, whether to check the input data frame for issues related to constructing the geometry of interese such as number of vertices per geometry. If FALSE, it will save a bit of time, which is useful when the input is already known to be good.
BPPARAM	Deprecated. The 'sfheaders' package is used in df2sf for much better performance.
...	Other arguments passed to 'sf::st_buffer', mainly to make polygon shapes, eg Visium spot 'endCapStyle = "ROUND"' and VisiumHD bin 'endCapStyle = "SQUARE"'

Value

An sf object.

Examples

# Points, use spotDiameter to convert to circle polygons
# This is done to Visium spots
pts_df <- readRDS(system.file("extdata/pts_df.rds",
    package = "SpatialFeatureExperiment"
))
sf_use <- df2sf(pts_df, geometryType = "POINT", spotDiameter = 0.1)
# Linestring
ls_df <- readRDS(system.file("extdata/ls_df.rds",
    package = "SpatialFeatureExperiment"
))
sf_use <- df2sf(ls_df, geometryType = "LINESTRING")
# Polygon
pol_df <- readRDS(system.file("extdata/pol_df.rds",
    package = "SpatialFeatureExperiment"
))
sf_use <- df2sf(pol_df,
    geometryType = "POLYGON",
    spatialCoordsNames = c("V1", "V2")
)
# Multipolygon
mpol_df <- readRDS(system.file("extdata/mpol_df.rds",
    package = "SpatialFeatureExperiment"
))
sf_use <- df2sf(mpol_df,
    geometryType = "MULTIPOLYGON",
    spatialCoordsNames = c("V1", "V2")
)
# Multiple sample_ids present
multipts_df <- readRDS(system.file("extdata/multipts_df.rds",
    package = "SpatialFeatureExperiment"
))
sf_use <- df2sf(multipts_df, geometryType = "MULTIPOINT")

pachterlab/SpatialFeatureExperiment documentation built on May 17, 2024, 12:24 a.m.