plotTrajectoryEvaluation | R Documentation |
Plots inferred gene expression along a spatial trajectory against model values.
plotTrajectoryEvaluation(
object,
id,
variables,
binwidth = getCCD(object),
n_bins_circle = NA_integer_,
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,
ncol = NULL,
nrow = 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. |
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 |
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 |
nrow , ncol |
Numeric values or NULL. Used to arrange multiple plots. |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
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