plotTrajectoryLineplotFitted | R Documentation |
Plots a trajectory lineplot in combination with models fitted to the course of the trajectory.
plotTrajectoryLineplotFitted(
object,
id,
variables,
binwidth = getCCD(object),
n_bins = NA_integer_,
model_subset = NULL,
model_remove = NULL,
model_add = NULL,
method_gs = NULL,
smooth_span = 0,
lineorder = c(1, 2, 3),
linesizes = c(1, 1, 1),
linecolors = c("forestgreen", "blue4", "red3"),
linetypes = c("solid", "solid", "dotted"),
display_residuals = TRUE,
area_alpha = 0.25,
display_points = TRUE,
pt_alpha = 0.9,
pt_size = 1.5,
nrow = NULL,
ncol = NULL,
force_grid = FALSE,
verbose = NULL,
...
)
object |
An object of class |
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(). |
smooth_span |
Numeric value. Controls the degree of smoothing.
Given to argument |
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. |
display_points |
Logical value. If set to TRUE points are used additionally to display the results. |
pt_alpha |
Numeric value. Specifies the degree of transparency of all points. |
pt_size |
Numeric value. Specifies the size of all points. |
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. |
A ggplot.
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