plotIasEvaluation | R Documentation |
Plots inferred gene expression along the distance to an image annotation against model values.
plotIasEvaluation(
object,
id,
variables,
distance = NA_integer_,
binwidth = ccDist(object),
n_bins_circle = NA_integer_,
angle_span = c(0, 360),
model_subset = NULL,
model_remove = NULL,
model_add = NULL,
pt_alpha = 0.9,
pt_color = "black",
pt_size = 1,
line_alpha = 0.9,
line_color = "blue",
line_size = 1,
display_se = FALSE,
display_corr = FALSE,
corr_p_min = 5e-05,
corr_pos_x = NULL,
corr_pos_y = NULL,
corr_text_sep = "\n",
corr_text_size = 1,
force_grid = FALSE,
bcsp_exclude = NULL,
verbose = NULL
)
object |
An object of class |
id |
Character value. The ID of the image annotation of interest. |
variables |
Character vector. All numeric variables (meaning genes, gene-sets and numeric features) that are supposed to be included in the screening process. |
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 |
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: |
n_bins_circle |
Numeric value or vector of length 2. Specifies how many times the area is buffered with the value
denoted in |
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.) |
model_subset |
Character value. Used as a regex to subset models.
Use |
model_remove |
Character value. Used as a regex to remove models are not supposed to be included. |
model_add |
Named list. Every slot in the list must be either a formula
containing a function that takes a numeric vector as input and returns a numeric
vector with the same length as its input vector. Or a numeric vector with the
same length as the input vector. Test models with |
pt_alpha |
Numeric value. Specifies the degree of transparency of all points. |
pt_size |
Numeric value. Specifies the size of all points. |
line_alpha |
Numeric. Affects alpha of main lines of the plot. |
line_color |
Character. Affects color of the main lines of the plot. |
line_size |
Numeric. Affects size of the main lines of the plot. |
display_corr |
Logical. If TRUE, correlation values are added to the plots. |
corr_p_min |
Numeric value. Everything below is displayed as <corr_p_min. |
corr_pos_x , corr_pos_y |
Numeric vector of length two. The position of the correlation text with x- and y-coordinates. |
corr_text_sep |
Character value used to separate correlation value and corresponding p-value. |
corr_text_size |
Numeric value. Size of text. |
force_grid |
Logical value. If |
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.) |
Several functions in SPATA2
have arguments that take distance input.
To specifically refer to a distance the unit must be specified. There are
three ways to create valid input for these arguments.
1. In pixel:
There are two valid input options to specify the distance in pixel:
numeric: Single numeric values, e.g. arg_input = c(2, 3.554, 69, 100.67)
. If no unit
is specified the input will be interpreted as pixels.
character: Suffixed with 'px', e.g. arg_input = c('2px', '3.554px', '69px', '100.67px')
Note: The unit pixel (px) is used for distances as well as for areas. If pixel refers to a distance the pixel side length is meant. If pixel refers to an area the number of pixels is meant.
2. According to the Systeme international d'unites (SI):
Specifying distances in SI units e.g. arg_input = c('2mm', '4mm')
etc.
requires the input to be a character as the unit must be provided as suffix.
Between the numeric value and the unit must be no empty space! Valid suffixes
can be obtained using the function validUnitsOfLengthSI()
.
3. As vectors of class unit
:
Behind the scenes SPATA2
works with the units
package. Input
is converted into vectors of class units
. Therefore, input can be directly
provided this way: arg_input = units::set_unit(x = c(2,4), value = 'mm')
Note that pixel is not a valid unit in the units
package. If you want
to specify the input in pixel you have to use input option 1. In pixel.
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