trelli_precheck {pmartR}

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.