getIasDf | R Documentation |
Extracts a data.frame of inferred gradients of numeric variables as a fucntion of distance to image annotations.
getIasDf(
object,
id,
distance = NA_integer_,
n_bins_circle = NA_integer_,
binwidth = getCCD(object),
angle_span = c(0, 360),
n_bins_angle = 1,
variables = NULL,
method_gs = NULL,
summarize_by = c("bins_angle", "bins_circle"),
summarize_with = "mean",
normalize_by = "sample",
normalize = FALSE,
remove_circle_bins = FALSE,
remove_angle_bins = FALSE,
rename_angle_bins = FALSE,
bcsp_exclude = NULL,
verbose = FALSE,
...
)
getImageAnnotationScreeningDf(...)
object |
An object of class |
id |
Character value. The ID of the image annotation of interest. |
distance |
Distance value. Specifies the distance from the border of the
image annotation to the horizon in the periphery up to which the screening
is conducted. (See details for more.) - See details of |
n_bins_circle |
Numeric value or vector of length 2. Specifies how many times the area is buffered with the value
denoted in |
binwidth |
Distance value. The width of the circular bins to which
the barcode-spots are assigned. We recommend to set it equal to the center-center
distance: |
angle_span |
Numeric vector of length 2. Confines the area screened by an angle span relative to the center of the image annotation. (See details fore more.) |
n_bins_angle |
Numeric value. Number of bins that are created by angle. (See details for more.) |
variables |
Character vector. All numeric variables (meaning genes, gene-sets and numeric features) that are supposed to be included in the screening process. |
method_gs |
Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA(). |
summarize_with |
Character value. Either 'mean' or 'median'. Specifies the function with which the bins are summarized. |
normalize |
Logical. If set to TRUE values will be scaled to 0-1. Hint: Variables that are uniformly expressed can not be scaled and are discarded. |
bcsp_exclude |
Character value containing name(s) of barcode-spots to be excluded from the analysis. |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
... |
Used to absorb deprecated arguments or functions. |
Data.frame.
library(SPATA2)
library(SPATAData)
data("image_annotations")
necrotic_img_ann <- image_annotations[["313_T"]][["necrotic_center"]]
object <- downloadSpataObject(sample_name = "313_T")
object <- setImageAnnotation(object = object, img_ann = necrotic_img_ann)
plotSurfaceIAS(
object = object,
id = "necrotic_center",
distance = 200
)
plotSurfaceIAS(
object = object,
id = "necrotic_center",
distance = 200,
binwidth = getCCD(object)*4, # lower resolution by increasing binwidth for visualization
n_bins_angle = 12,
display_angle = TRUE
)
getIasDf(
object = object,
id = "necrotic_center",
distance = 200,
variables = "VEGFA"
)
getIasDf(
object = object,
id = "necrotic_center",
distance = 200,
variables = "VEGFA"
)
getIasDf(
object = object,
id = "necrotic_center",
distance = 200,
variables = "VEGFA",
n_bins_angle = 12
)
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