trelli_precheck: Performs initial checks for trelliData objects

In pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Performs initial checks for trelliData objects

Description

This function runs necessary checks for pmartR trelliscope plotting functions. It cleans any parameters (rounding numerics to integers, etc.), and returns them.

Usage

trelli_precheck(
  trelliData,
  trelliCheck,
  cognostics,
  acceptable_cognostics,
  ggplot_params,
  interactive,
  test_mode,
  test_example,
  single_plot,
  seqDataCheck,
  seqText = NULL,
  p_value_skip = FALSE,
  p_value_thresh = NULL
)

Arguments

trelliData	trelliData object the user passed to a plotting function
trelliCheck	Check if the object type is supposed to be "omics", "statRes" or put a vector of both
cognostics	A vector of the user provided cognstics
acceptable_cognostics	The acceptable cognostics for this plot
ggplot_params	The vector of user provided ggplots
interactive	The user provided logical for whether the plot should be interactive
test_mode	The user provided logical for whether a smaller trelliscope should be returned
test_example	The user provided vector of plot indices
single_plot	The user provided logical for whether a single plot should be returned
seqDataCheck	Whether seqData is permitted for this plot. "no" means that seqData cannot be used at all, "permissible" means that seqData can be used, and "required" means that seqData is required for the plotting function.
seqText	Text that should appear when seqDataCheck is violated.
p_value_skip	Whether to skip specific p_value checks.
p_value_thresh	The user provided threshold for plotting significant p-values.

Value

No return value, validates a trelliData object before passing it to builder functions.

pmartR documentation built on Oct. 15, 2024, 1:06 a.m.