getImageAnnotations | R Documentation |
ImageAnnotation
-objectsExtracts a list of objects of class ImageAnnotaion
.
getImageAnnotations(
object,
ids = NULL,
tags = NULL,
test = "any",
add_barcodes = TRUE,
strictly = FALSE,
add_image = TRUE,
expand = 0,
square = FALSE,
flatten = FALSE,
check = FALSE
)
object |
An object of class |
ids |
Character vector or |
tags |
Character vector or |
test |
Character value. One of any. all, identical, not_identical and
none. Specifies how input for |
add_barcodes |
Logical. If |
strictly |
Logical. If |
add_image |
Logical. If TRUE, the area of the histology image that
is occupied by the annotated structure is added to the |
expand |
Specifies image expansion. An image that is cropped based on an image
annotation centers around the image annotation. If |
square |
Logical value. Most image annotations come in variable shapes and
have different horizontal and vertical diameters. Therefore, height and width of the image
section are usually not equal. If Processing of the image output depending on argument |
A list of objects of class ImageAnnotation
.
The argument expand
is a versatile way, to specify how a cropped
image section is extracted. If you want the cropped image as is, specify
expand = 0
. Else, there are multiple options. In general, expand
takes
three kinds of values, namely percentages, distances and distance exclamations.
Percentage: A string suffixed with %. E.g. expand = '50%'
adds 50% of the distance from the center to the border of the image annotation
to the image frame.
Distance measures: In pixel or European units of length. E.g. expand = list(x = '1mm')
expands the x-axis on both sides with 1mm. expand = list(x = c('0.5mm', 1.5mm')
expands the x-axis on the left side with 0.5mm and on the right side with 1.5mm.
Exclam distance measures: Distance measure with an exclamation mark
suffix. E.g. expand = '1mm!'
centers the image and forces an axis length of
1 millimeter. (Example 5)
Depending on how the values are specified different parts of the image can be expanded.
Single values, like expand = 50
, are recycled: Every end of each image axis
is expanded by 50 pixel. (Example 2)
Vectors of length two, like expand = c('1mm', '2mm')
, are recycled: The beginning
of each axis is expanded by 1 millimeter. The end of each axis is expanded by
2mm. (Example 3)
Named lists can be more precise. expand = list(x = c('1mm', '0.5mm'), y = c('0.25mm', '1mm'))
.
Applies the vectors to expand the corresponding axis. (Example 4)
Using exclam input the side of the axis must not be specified as the
axis is fixed as a whole. E.g expand = list(x = '1mm!', y = '2mm!')
results
in the same output as expand = list(x = c('1mm!', '1mm!'), y = c('2mm!', '2mm!')
.
Input for argument tags
specifies the tags of interest.
Argument test
decides about how the specified tags are used to select
the image annotations of interest. There are multiple options:
Argument test
set to 'any' or 1: To be included, an image annotation
must be tagged with at least one of the input tags.
Argument test
set to 'all' or 2: To be included, an image annotation
must be tagged with all of the input tags. Can contain tags that are not specified.
Argument test
set to 'identical' or 3: To be included, an image annotation
must be tagged with all of the input tags. Can not be tagged with anything else.
Argument test
set to not_identical or 4: To be included, an image
annotation must not be tagged with the combination of input tags.
Argument test
set to 'none' or 5: To be included, an image annotation
must not contain any of the input tags.
Note that the filtering process happens after the filtering by input for argument
ids
. You can first select a group of image annotations by naming their IDs
and then select among them via tags and test. If ids
is NULL
, you select
among all image annotations via tags and test. And if tags
is also NULL
,
the function uses all image annoations.
To test how the extracted image section looks like depending
on input for argument square
and expand
use
plotImageAnnotations(..., encircle = FALSE)
.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.