Plot surrogate variables for svaEnmix — plotSvaEnmix • dnaEPICO

Draw one of the standard surrogate-variable plots used by svaEnmix().

plotSvaEnmix(
  analysisData,
  plot = c("sentrix_id", "sentrix_position", "matrix"),
  display = FALSE,
  file = NULL,
  width = 2000L,
  height = 1000L,
  res = 150L,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_plotSvaEnmix.txt"
)

Arguments

analysisData: Object returned by analyzeSvaEnmix().
plot: Character. Plot type: "sentrix_id", "sentrix_position", or "matrix".
display: Logical. If TRUE, draw the plot on the active graphics device.
file: Character or NULL. TIFF file path used for saved output.
width: Integer. Plot width in pixels when file is supplied.
height: Integer. Plot height in pixels when file is supplied.
res: Integer. TIFF resolution in DPI when file is supplied.
verbose: Logical. If TRUE, emit progress messages with message().
logs: Logical. If TRUE, write the same messages to a log file.
log_dir: Character or NULL. Directory used for the log file when logs = TRUE.
log_file: Character. File name used when logs = TRUE.

Value

Invisibly returns file when a TIFF is written, otherwise NULL.

Examples

ex <- dnaEPICO:::exampleSvaAnalysisStateDnaEpico()
plotSvaEnmix(
  analysisData = ex$analysisData,
  plot = "sentrix_id",
  display = FALSE,
  verbose = FALSE,
  logs = FALSE
)