getPixelDf.Rd
Extracts a data.frame in which each row corresponds to a pixel in the current image with x- and y-coordinates.
getPixelDf(object, ...)
# S4 method for class 'SPATA2'
getPixelDf(
object,
img_name = activeImage(object),
colors = FALSE,
hex_code = FALSE,
content = FALSE,
transform = TRUE,
xrange = NULL,
yrange = NULL,
scale_fct = 1
)
# S4 method for class 'SpatialData'
getPixelDf(
object,
img_name = activeImage(object),
colors = FALSE,
hex_code = FALSE,
content = FALSE,
xrange = NULL,
yrange = NULL,
transform = TRUE,
scale_fct = 1,
...
)
# S4 method for class 'HistoImage'
getPixelDf(
object,
colors = FALSE,
hex_code = FALSE,
content = FALSE,
xrange = NULL,
yrange = NULL,
transform = TRUE,
scale_fct = 1,
...
)
# S4 method for class 'Image'
getPixelDf(
object,
colors = FALSE,
hex_code = FALSE,
use_greyscale = FALSE,
frgmt_threshold = c(5e-04, 0.01),
eps = 1,
minPts = 3,
...
)
An object of class SPATA2
or, in case of S4 generics,
objects of classes for which a method has been defined.
Used to absorb deprecated arguments or functions.
Character value. The name of the image of interest.
If NULL
, the active image is chosen by default. Either way, must
be one of getImageNames()
.
Logical value. If TRUE
, adds all colors from the image
as variables named col1-col.n where n is the number of colors.
Logical value. Ignored if no images exist in the object. If TRUE
,
spatial transformation instructions saved during image alignment of
the image img_name
are applied. Only relevant if there are any images registered
in the SPATA2
object.
Distance vector of length
two or NULL
. If not NULL
, specifies the x- and y-range to which
the spatial output is cropped. E.g. xrange = c(200, 500)
results in
the two dimensional space being cropped from x-coordinate 200px up to
x-coordinate 500px. If NULL
, the original range is used.
Distance measure. Given to eps
of dbscan::dbscan()
. Determines
the size (radius) of the epsilon neighborhood.
Numeric value. Given to dbscan::dbscan()
. Determines the
number of minimum points required in the eps neighborhood for core points
(including the point itself)
Logical value. If TRUE
, adds a variable called pxl_group
that indicates whether the pixel is placed on a contiguous tissue section, on
artefact tissue fragments or on background.
Data.frame.