Plots calibration curves for each measured feature.

Usage

plot_calibrationcurves(
  data = NULL,
  variable = "intensity",
  overwrite_metadata = FALSE,
  fit_method = c("linear", "quadratic"),
  fit_weighting = c(NA, "none", "1/x", "1/x^2"),
  log_axes = FALSE,
  filter_data = FALSE,
  output_pdf = FALSE,
  include_feature_filter = "",
  exclude_feature_filter = "",
  max_regression_value = NA,
  path = "",
  rows_page = 4,
  cols_page = 5,
  specific_page = NA,
  point_size = 1.5,
  line_width = 0.7,
  scaling_factor = 1,
  page_orientation = "LANDSCAPE",
  font_base_size = 7,
  show_progress = TRUE,
  return_plots = FALSE
)

Arguments

data: A MidarExperiment object .
variable: The variable name to plot on the y-axis, usually a measure of intensity. Defaults to "intensity"
overwrite_metadata: A logical value (TRUE or FALSE). If TRUE, the function will ignore any fit method and weighting settings defined in the metadata and use the provided fit_method and fit_weighting values for all analytes.
fit_method: A character string specifying the default regression fit method to use for the calibration curve. Must be one of "linear" or "quadratic". This method will be applied if no specific fit method is defined for a feature in the metadata.
fit_weighting: A character string specifying the default weighting method for the regression points in the calibration curve. Must be one of "none", "1/x", or "1/x^2". This method will be applied if no specific weighting method is defined for a feature in the metadata.
log_axes: Logical. If TRUE, the x and y axes are displayed in logarithmic scale. Defaults to FALSE.
filter_data: Logical. Indicates whether to use quality control (QC) filtered data (TRUE) or the raw data (FALSE). Defaults to FALSE.
output_pdf: Logical. If TRUE, saves the generated plots as a PDF file. Defaults to FALSE.
include_feature_filter: A regex pattern to filter and include features that match the criteria. If omitted, all features are considered.
exclude_feature_filter: A regex pattern to filter and exclude features that match the criteria. If omitted, no features are excluded.
max_regression_value: The maximum x value (analyzed amount) for which the regression line is fitted. Defaults to NA, considering all data points.
path: The file path for saving the PDF. Defaults to an empty string, meaning no file is saved.
rows_page: The number of rows of plots per page for the PDF output. Defaults to 4.
cols_page: The number of columns of plots per page for the PDF output. Defaults to 5.
specific_page: An integer specifying a particular page to plot. If NA, all pages are plotted.
point_size: Numeric value specifying the size of points in the plot. Defaults to 1.5.
line_width: Numeric value specifying the width of regression lines. Defaults to 0.7.
scaling_factor: A universal scaling factor for fonts, symbols, and lines. Defaults to 1.
page_orientation: The orientation of the PDF paper, either "LANDSCAPE" or "PORTRAIT". Defaults to "LANDSCAPE".
font_base_size: The base font size for text in the plots. Defaults to 7.
show_progress: Logical. Show a progress bar during plot creation if set to TRUE. Defaults to TRUE.
return_plots: Logical. If TRUE, returns the plots as a list of ggplot2 objects. Each item represents a page of plots. Defaults to FALSE.

Value

If return_plots is TRUE, a list of ggplot2 objects is returned. Otherwise, the function may return a plot output and/or save a PDF, depending on the output_pdf parameter.