ifcb_psd_plot {iRfcb} | R Documentation |
Generate PSD Plot for a Given Sample
Description
This function generates a plot for a given sample from Particle Size Distribution (PSD) data and fits from Imaging FlowCytobot (IFCB).
The PSD data and fits can be generated by ifcb_psd
(Hayashi et al. in prep).
Usage
ifcb_psd_plot(sample_name, data, fits, start_fit)
Arguments
sample_name |
The name of the sample to plot in DYYYYMMDDTHHMMSS. |
data |
A data frame containing the PSD data (data output from |
fits |
A data frame containing the fit parameters for the power curve (fits output from |
start_fit |
The x-value threshold below which data should be excluded from the plot and fit. |
Value
A ggplot object representing the PSD plot for the sample.
References
Hayashi, K., Walton, J., Lie, A., Smith, J. and Kudela M. Using particle size distribution (PSD) to automate imaging flow cytobot (IFCB) data quality in coastal California, USA. In prep.
See Also
ifcb_psd
https://github.com/kudelalab/PSD
Examples
## Not run:
#' # Initialize a python session if not already set up
ifcb_py_install()
# Analyze PSD
psd <- ifcb_psd(feature_folder = 'path/to/features',
hdr_folder = 'path/to/hdr_data',
save_data = TRUE,
output_file = 'psd/svea_2021',
plot_folder = NULL,
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)
# Plot PSD of the first sample
plot <- ifcb_psd_plot(sample_name = "D20230316T101514",
data = psd$data,
fits = psd$fits,
start_fit = 10)
# Inspect plot
print(plot)
## End(Not run)