ifcb_adjust_classes: Adjust Classifications in Manual Annotations

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

Adjust Classifications in Manual Annotations

Description

This function adjusts the classifications in manual annotation files based on a class2use file. It loads a specified class2use file and applies the adjustments to all relevant files in the specified manual folder. Optionally, it can also perform compression on the output files. This is the R equivalent function of start_mc_adjust_classes_user_training from the ⁠ifcb-analysis repository⁠ (Sosik and Olson 2007).

Usage

ifcb_adjust_classes(class2use_file, manual_folder, do_compression = TRUE)

Arguments

class2use_file	A character string representing the full path to the class2use file (should be a .mat file).
manual_folder	A character string representing the path to the folder containing manual annotation files. The function will look for files starting with 'D' in this folder.
do_compression	A logical value indicating whether to apply compression to the output files. Defaults to TRUE.

Details

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

Value

None

References

Sosik, H. M. and Olson, R. J. (2007), Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol. Oceanogr: Methods 5, 204–216.

See Also

ifcb_py_install ifcb_create_class2use https://github.com/hsosik/ifcb-analysis

Examples

## Not run: 
# Initialize a python session if not already set up
ifcb_py_install()

ifcb_adjust_classes("data/config/class2use.mat",
                    "data/manual/2014/")

## End(Not run)

iRfcb documentation built on April 16, 2025, 1:09 a.m.