plotTrajectoryFit: Display trajectory fit

In kueckelj/SPATA: A Toolbox for Spatial Gene Expression Analysis

Display trajectory fit

Description

Displays the trend of a trajectory in comparison to a variety of models / mathematical curves.

Usage

plotTrajectoryFit(
  object,
  trajectory_name,
  of_sample = "",
  variable,
  method_gs = "mean",
  accuracy = 5,
  display_residuals = FALSE,
  verbose = TRUE,
  ...
)

Arguments

object	A valid spata-object.
trajectory_name	The trajectory of interest specified as a single character value.
of_sample	The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen.
variable	The gene or gene set of interest specified as a character value.
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().
accuracy	Numeric. Given to accuracy-argument of plyr::round_any(). Determines how many barcode-spots will be summarized as one sub-trajectory-part.
display_residuals	Logical. If set to TRUE the residuals are displayed via a red line.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)
...	Additional parameters given to ggplot2::facet_wrap().

Value

Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.