Plot IAS evaluation per variable-model pair

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
)

Arguments

object

An object of class spata2.

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 ?is_dist for more information about distance values.

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: binwidth = getCCD(object). (See details for more.) - See details of ?is_dist for more information about distance values.

n_bins_circle

Numeric value or vector of length 2. Specifies how many times the area is buffered with the value denoted in binwidth. (See details for more.)

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 validModelNames() to obtain all model names that are known to SPATA2 and showModels() to visualize them.

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 showModels().

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 TRUE, facet_grid() is used regardless of variables being of length 1.

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.)

Distance measures

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.