plotIasLineplotFitted | R Documentation |
Plots an IAS lineplot in combination with models fitted to the binned distance towards the image annotation.
plotIasLineplotFitted(
object,
id,
variables,
distance,
binwidth = getCCD(object),
n_bins = NA_integer_,
model_subset = NULL,
model_remove = NULL,
model_add = NULL,
method_gs = NULL,
lineorder = c(1, 2, 3),
linesize = 1,
linecolors = c("forestgreen", "blue4", "red3"),
linetypes = c("solid", "solid", "dotted"),
display_residuals = TRUE,
area_alpha = 0.25,
nrow = NULL,
ncol = NULL,
force_grid = FALSE,
verbose = NULL,
...
)
object |
An object of class |
id |
Character value. The ID of the image annotation of interest. |
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 |
Numeric value. Specifies the exact number of bins the barcodes are binned into. |
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 |
method_gs |
Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA(). |
linesize |
Numeric value. The size of the line(s) plotted. |
linecolors , linetypes |
The colors and types of the three lines. First value stands for the values of the variable, second on for the models, third one for the residuals. |
display_residuals |
Logical value. If TRUE, the residuals curve is displayed. |
area_alpha |
Numeric value. The alpha value for the area under the curve of the resiudals. |
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.) |
... |
Used to absorb deprecated arguments or functions. |
The method for class ImageAnnotationScreening
(the output of
the function imageAnnotationScreening()
) can be used
to show the area on which the results base. Therefore, it does not have
arguments binwidth
, n_bins_circle
and n_bins_angle
.
An invisible list of ggplots.
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