Plot Response Curves — plot_responsecurves • midar

This function plots response curves for each feature. Multiple response curves, each with a linear regression line, can be plotted on the same graph. Each feature is displayed as a separate facet.

Usage

plot_responsecurves(
  data = NULL,
  variable = "intensity",
  filter_data = FALSE,
  include_qualifier = TRUE,
  include_istd = TRUE,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  max_regression_value = NA,
  output_pdf = FALSE,
  path = NA,
  return_plots = FALSE,
  color_curves = NULL,
  point_size = 1.5,
  line_width = 0.7,
  font_base_size = 7,
  rows_page = 4,
  cols_page = 5,
  specific_page = NA,
  page_orientation = "LANDSCAPE",
  show_progress = TRUE
)

Arguments

data: A MidarExperiment object containing the dataset and metadata.
variable: The variable to plot on the y-axis.
filter_data: Whether to use all data (default) or only QC-filtered data (filtered via filter_features_qc()).
include_qualifier: Logical, whether to include qualifier features. Default is TRUE.
include_istd: Logical, whether to include internal standard (ISTD) features. Default is TRUE.
include_feature_filter: A regex pattern or a vector of feature names used to filter features by feature_id. If NA or an empty string ("") is provided, the filter is ignored. When a vector of length > 1 is supplied, is supplied, only features with exactly these names are selected (applied individually as OR conditions).
exclude_feature_filter: A regex pattern or a vector of feature names to exclude features by feature_id. If NA or an empty string ("") is provided, the filter is ignored. When a vector of length > 1 is supplied, is supplied, only features with exactly these names are excluded (applied individually as OR conditions).
max_regression_value: The maximum sample_amount (x) value for fitting the regression line. If NA, regression is based on all data points.
output_pdf: If TRUE, saves the generated plots as a PDF file. Wjen FALSE, plots are directly plotted.
path: The file path for saving the PDF. Must be defined if output_pdf is TRUE.
return_plots: Logical. If TRUE, returns the plots as a list of ggplot2 objects.
color_curves: A vector of colors for the curves. If NULL (default), the colors for each curve are generated automatically. If colors are provided, the number of colors must match the number of curves.
point_size: Size of points in millimeters.
line_width: Width of regression lines.
font_base_size: Base font size for text. Default is 7.
rows_page: Number of rows of plots per page.
cols_page: Number of columns of plots per page.
specific_page: An integer specifying a specific page to plot. If NA (default), all pages are plotted.
page_orientation: Orientation of the PDF paper: "LANDSCAPE" or "PORTRAIT".
show_progress: Logical. If TRUE, displays a progress bar during plot creation.

Value

If return_plots is TRUE, a list of ggplot2 objects is returned. Otherwise, the function saves the plot output or does not return anything.

Details

Features for plotting can be filtered using QC filters defined via filter_features_qc() or through include_feature_filter and exclude_feature_filter arguments. The resulting plots offer extensive customization options, including point size, line width, point color, point fill, point shape, line color, ribbon fill, and font base size.

Plots will be divided into multiple pages if the number of features exceeds the product of rows_page and cols_page settings. The function supports both direct plotting within R and saving plots as PDF files. Additionally, plots can be returned as a list of ggplot2 objects for further manipulation or integration into other analyses.