Plot Response Curves — plot_responsecurves • midar

Generates linear regression plots for each measured feature within a dataset. The function allows for customization of the plot's appearance and format, and it can filter features based on specified criteria.

Usage

plot_responsecurves(
  data = NULL,
  variable = "intensity",
  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 containing the dataset with sample amounts and detector signals. Required.
variable: The variable name to plot on the y-axis, usually a measure of intensity. Defaults to "intensity".
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.