Create a Run Scatter Plot to Visualize Analyte Distributions

The run scatter plot allows you to visualize the sequence of measurements and distribution of QC (sample) types across the analysis run sequence. This can be useful for identifying trends, outliers, or other patterns in the data.

The function provides a range of options for customizing the plot, such as:

Filtering the data (e.g., by QC type, feature ID)
Applying outlier capping
Displaying batch information and control limits
Showing trend lines for drift correction
Controlling the layout and appearance of the plot

Usage

plot_runscatter(
  data = NULL,
  variable = c("intensity", "norm_intensity", "conc", "conc_raw", "area", "height",
    "fwhm"),
  filter_data = FALSE,
  qc_types = NA,
  include_qualifier = TRUE,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  plot_range_indices = NA,
  output_pdf = FALSE,
  path = "",
  log_scale = FALSE,
  cap_outliers = FALSE,
  cap_qc_k_mad = 4,
  cap_spl_k_mad = 4,
  cap_top_n_values = NA,
  show_batches = TRUE,
  show_control_limits = NA,
  set_limits_n_sd = NA,
  limits_batchwise = FALSE,
  limits_linecolor = "#38dff5",
  limits_linewidth = 0.75,
  batches_as_shades = FALSE,
  batch_line_color = "#b6f0c5",
  batch_shading_color = "grey93",
  cols_page = 3,
  rows_page = 3,
  base_font_size = 11,
  annot_scale = 1,
  show_trend = FALSE,
  trend_linecolor = "#22e06b",
  fit_qc_type = "BQC",
  page_orientation = "LANDSCAPE",
  point_transparency = 1,
  point_size = 2,
  point_border_width = 1,
  specific_page = NA,
  y_label_text = NA,
  return_plots = FALSE,
  show_gridlines = FALSE,
  show_progress = FALSE
)

Arguments

data: MidarExperiment object
variable: Variable to plot, one of 'area', 'height', 'intensity', 'norm_intensity', 'intensity_raw', 'norm_intensity_raw', 'response', 'conc', 'conc_raw', 'rt', 'fwhm.'
filter_data: Logical, whether to use QC-filtered data based on criteria set via filter_features_qc()
qc_types: QC types to be shown. Can be a vector of QC types or a regular expression pattern. NA (default) displays all available QC/Sample types.
include_qualifier: Logical, whether to include qualifier features
include_feature_filter: Regex pattern to select features by feature_id. NA or "" ignores the filter.
exclude_feature_filter: Regex pattern to exclude features by feature_id. NA or "" ignores the filter.
plot_range_indices: Numeric vector of length 2, specifying the start and end indices of the sequence to be plotted. NA plots all samples.
output_pdf: Logical, whether to save the plot as a PDF file
path: File name for the PDF output
log_scale: Logical, whether to use a log10 scale for the y-axis
cap_outliers: Logical, whether to cap upper outliers based on MAD fences of SPL and QC samples
cap_qc_k_mad: Numeric, k * MAD (median absolute deviation) for outlier capping of QC samples
cap_spl_k_mad: Numeric, k * MAD (median absolute deviation) for outlier capping of SPL samples
cap_top_n_values: Numeric, cap the top n values regardless of MAD fences. NA or 0 ignores this filter.
show_batches: Logical, whether to show batch separators in the plot
show_control_limits: Logical, whether to show the mean line for the specified QC types. NA ignores the mean line.
set_limits_n_sd: Numeric, show +/- n x SD lines for the QC types defined in show_control_limits. NA ignores the SD lines.
limits_batchwise: Logical, whether to calculate the mean and SD lines per batch
limits_linecolor: Color of the mean and SD lines
limits_linewidth: Width of the mean and SD lines
batches_as_shades: Logical, whether to show batches as shaded areas instead of line separators
batch_line_color: Color of the batch separator lines
batch_shading_color: Color of the batch shaded areas
cols_page: Number of columns per page
rows_page: Number of rows per page
base_font_size: Base font size for the plot
annot_scale: Scale factor for text elements
show_trend: Logical, whether to show a drift correction trend line
trend_linecolor: Color of the trend line
fit_qc_type: QC type used for smoothing the trend line
page_orientation: Page orientation, "LANDSCAPE" or "PORTRAIT"
point_transparency: Alpha transparency of the data points
point_size: Size of the data points
point_border_width: Width of the data point borders
specific_page: Integer, show/save a specific page number. NA plots/saves all pages.
y_label_text: Override the default y-axis label text
return_plots: Logical, whether to return the list of ggplot objects
show_gridlines: Logical, whether to show major x and y gridlines
show_progress: Logical, whether to show a progress bar

Value

A list of ggplot2 plots, or NULL if return_plots = FALSE