ifcb_psd: Plot and Save IFCB PSD Data

Description

This function generates and saves data about a dataset's Particle Size Distribution (PSD) from Imaging FlowCytobot (IFCB) feature and hdr files, which can be used for data quality assurance and quality control.

Usage

ifcb_psd(
  feature_folder,
  hdr_folder,
  bins = NULL,
  save_data = FALSE,
  output_file = NULL,
  plot_folder = NULL,
  use_marker = FALSE,
  start_fit = 10,
  r_sqr = 0.5,
  beads = NULL,
  bubbles = NULL,
  incomplete = NULL,
  missing_cells = NULL,
  biomass = NULL,
  bloom = NULL,
  humidity = NULL,
  micron_factor = 1/3.4,
  fea_v = 2,
  use_plot_subfolders = TRUE,
  ...
)

Value

A list containing three tibbles:

data: A tibble with flattened PSD data for each sample.
fits: A tibble containing curve fit parameters for each sample.
flags: A tibble of flags for each sample, or NULL if no flags are found.

The save_data parameter only controls whether CSV files are written to disk; the function always returns this list.

Arguments

feature_folder: The absolute path to a directory containing all of the feature files for the dataset (version can be defined in fea_v).
hdr_folder: The absolute path to a directory containing all of the hdr files for the dataset.
bins: An optional character vector of bin names (e.g., "D20251021T133007_IFCB134") to restrict processing to a specified subset of bins. If NULL (default), all bins present in feature_folder are processed.
save_data: A boolean indicating whether to save data to CSV files. Default is FALSE.
output_file: A string with the base file name for the .csv output (including path). Set to NULL to avoid saving data (default).
plot_folder: The folder where graph images for each sample will be saved. If NULL (default), plots are not saved. If use_plot_subfolders = TRUE, plots are organized into subfolders based on their flag status.
use_marker: A boolean indicating whether to show markers on the plot. Default is FALSE.
start_fit: An integer indicating the start fit value for the plot. Default is 10.
r_sqr: The lower limit of acceptable R^2 values (any curves below it will be flagged). Default is 0.5.
beads: The maximum multiplier for the curve fit. Any files with higher curve fit multipliers will be flagged as bead runs. If this argument is included, files with "runBeads" marked as TRUE in the header file will also be flagged. Optional.
bubbles: The minimum difference between the starting ESD and the ESD with the most targets. Files with a difference higher than this threshold will be flagged as mostly bubbles. Optional.
incomplete: A numeric vector of length 2 giving the minimum volume of cells (in c/L) and the minimum mL analyzed for a complete run. Files with values below these thresholds will be flagged as incomplete. Optional.
missing_cells: The minimum image count ratio threshold. Files with ratios below this value will be flagged as missing cells. Optional.
biomass: The minimum number of targets in the most populated ESD bin for any given run. Files with fewer targets will be flagged as low biomass. Optional.
bloom: The minimum difference between the starting ESD and the ESD with the most targets. Files with a difference less than this threshold will be flagged as bloom events. This threshold is usually lower than the bubbles threshold. Optional.
humidity: The maximum percent humidity. Files with higher values will be flagged as high humidity. Optional.
micron_factor: The conversion factor to microns. Default is 1/3.4.
fea_v: The version number of the IFCB feature file (e.g., 2, 4). Default is 2, as described in Hayashi et al. 2025.
use_plot_subfolders: A boolean indicating whether to save plots in subfolders based on the sample's flag status. If TRUE (default), samples without flags are saved in a "PSD.OK" subfolder, and samples with flags are saved in subfolders named after their flag(s). If FALSE, all plots are saved directly in plot_folder.
...: Additional arguments passed to ggsave(). These override the default width, height, dpi, and background color when saving plots. For example, width = 7, dpi = 300 can be supplied.

Details

The PSD function originates from the PSD Python repository (Hayashi et al. 2025), which can be found at https://github.com/kudelalab/PSD.

Python must be installed to use this function. The required Python packages can be installed in a virtual environment using ifcb_py_install().

References

Hayashi, K., Enslein, J., Lie, A., Smith, J., Kudela, R.M., 2025. Using particle size distribution (PSD) to automate imaging flow cytobot (IFCB) data quality in coastal California, USA. International Society for the Study of Harmful Algae. https://doi.org/10.15027/0002041270

Examples

Run this code

if (FALSE) {
# Initialize the Python session if not already set up
ifcb_py_install()

ifcb_psd(
  feature_folder = 'path/to/features',
  hdr_folder = 'path/to/hdr_data',
  bins = c("D20211021T133007_IFCB134", "D20211021T140753_IFCB134"),
  save_data = TRUE,
  output_file = 'psd/svea_2021',
  plot_folder = 'psd/plots',
  use_marker = FALSE,
  start_fit = 13,
  r_sqr = 0.5,
  beads = 10 ** 9,
  bubbles = 150,
  incomplete = c(1500, 3),
  missing_cells = 0.7,
  biomass = 1000,
  bloom = 5,
  humidity = NULL,
  micron_factor = 1/2.77,
  fea_v = 2
)
}

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