getImgAnnSummaryDf.RdExtracts information about image annotations in a data.frame.
getImgAnnSummaryDf(
object,
ids = NULL,
area = TRUE,
unit_area = "mm2",
center = TRUE,
unit_center = "px",
genes = NULL,
summarize_with = "mean",
tags_to_lgl = TRUE,
tags_keep = FALSE,
verbose = NULL
)An object of class spata2.
Character vector or NULL. If character, specifies the IDs
of the image annotations of interest. If numeric, the image annotations are picked by number.
If NULL, all image annotations are included - subsequent selection with tags and
test is possible.
Logical. If TRUE, the area of each image annotation
is added in a variable named area.
The unit of the area variable.
Logical. If TRUE, two variables named center_x and
center_y area added providing the center coordinates of the image
annotation.
The unit of the center variables.
Character value or NULL. If character, the gene expression
of the named genes is summarized among all barcode spots that fall in the
area of the image annotation and are added as a variable.
Character value. The summarizing function with which the gene expression values are summarized.
Logical. If TRUE, tag information is displayed in logical
variables where each variable is named like one of the unique tags and
every value is either TRUE if the annotation cotnains the tag or FALSE
if not.
Logical. If TRUE, variable tags is not removed if
tags_to_lgl is TRUE.
Logical. If set to TRUE informative messages regarding the computational progress will be printed.
(Warning messages will always be printed.)
Data.frame in which each row corresponds to an image annotation identified by the variable id.