plotting_utility: plotting_utility helper function

In rBiasCorrection: Correct Bias in DNA Methylation Analyses

plotting_utility helper function

Description

Internal function to carry out the plotting of the calibrations curves.

Usage

plotting_utility(
  data,
  plotlist_reg,
  type,
  samplelocusname,
  locus_id = NULL,
  rv,
  mode = NULL,
  plotdir,
  logfilename,
  minmax,
  plot_height = 5,
  plot_width = 7.5,
  plot_textsize = 1
)

Arguments

data	A data.table object that contains the calibration data.
plotlist_reg	A list object contating regression plots without regression curves (output of regression_utility()).
type	A single integer. Type of data to be corrected: either "1" (one locus in many samples, e.g. pyrosequencing data) or "2" (many loci in one sample, e.g. next-generation sequencing data or microarray data).
samplelocusname	A character string. In type 1 data: locus name - name of the gene locus under investigation. In type 2 data: sample name - name of the sample under investigation.
locus_id	A character string. Default: NULL. ID of the respective locus (only used in type 2 correction).
rv	A list object. A list that contains additional objects needed for the algorithms.
mode	A character string. Default: NULL. Used to indicate "corrected" calibration data.
plotdir	A character string. Path to the folder, where plots are saved.
logfilename	A character string. Path to a file to save the log messages (default = paste0(tempdir(), "/log.txt")).
minmax	A logical, indicating which equations are used for BiasCorrection (default: FALSE). If TRUE, equations are used that include the respective minima and maxima of the provided data.
plot_height	A integer value. The height (unit: inch) of the resulting plots (default: 5).
plot_width	A integer value. The width (unit: inch) of the resulting plots (default: 7.5).
plot_textsize	A integer value. The textsize of the resulting plots (default: 16).

Value

This function creates calibration plots and writes them to the local filesystem.

Examples

# define list object to save all data
rv <- list()
rv$minmax <- TRUE
rv$selection_method <- "RelError"
rv$sample_locus_name <- "Test"
rv$seed <- 1234

# define logfilename
logfilename <- paste0(tempdir(), "/log.txt")

# define plotdir
rv$plotdir <- paste0(tempdir(), "/plots/")
dir.create(rv$plotdir)

# import experimental file
exp_type_1 <- rBiasCorrection::example.data_experimental
rv$fileimport_experimental <- exp_type_1$dat

# import calibration file
cal_type_1 <- rBiasCorrection::example.data_calibration
rv$fileimport_calibration <- cal_type_1$dat
rv$vec_cal <- cal_type_1$vec_cal


# perform regression
regression_results <- regression_utility(
  rv$fileimport_calibration,
  "Testlocus",
  locus_id = NULL,
  rv = rv,
  mode = NULL,
  logfilename,
  minmax = rv$minmax,
  seed = rv$seed
)

# extract the plotlist
plotlist_reg <- regression_results$plot_list

plotting_utility(
  data = rv$fileimport_calibration,
  plotlist_reg = plotlist_reg,
  type = 1,
  samplelocusname = rv$sample_locus_name,
  locus_id = NULL,
  rv = rv,
  mode = NULL,
  plotdir = rv$plotdir,
  logfilename = logfilename,
  minmax = rv$minmax,
  plot_height = 5,
  plot_width = 7.5,
  plot_textsize = 1
)

rBiasCorrection documentation built on June 21, 2022, 1:05 a.m.