bs5_nc: gates out or assign indicators to Synechococcus cyanobacteria...

Description Usage Arguments Details

View source: R/bs5_nc.R

Description

This function takes in a flowframe with debris removed and identifies ynechococcus cyanobacteria cell population in the provided frame.

Usage

1
bs5_nc(bs4bs5, p1, p2, others, to_retain = "potential")

Arguments

bs4bs5

flowframe with debris (left) removed.

p1

first flowcytometer channel that can be used to separate cells of interest from the rest, e.g. "RED.B.HLin".

p2

second flowcytometer channel that can be used to separate cells of interest from the rest, e.g. "YEL.B.HLin"

others

row numbers for non-debris events. This is provided by the debris_nc or debris_inc function.

to_retain

should potential candidates be retained or further gating be applied to filter out only certain Synechococcus cyanobacteria cells. @return list containing;

  • syn_reduced - flowframe containing only BS5s

  • others_nk - unidentified particle positions

  • syn_pos - Synechococcus cyanobacteria cells positions

  • others_nk2 - other unidentified particle positions

Details

The function uses the getPeaks and deGate functions in the flowDensity package to identify peaks and identify cut-off points between these peaks. This function is not designed to be called in isolation, if called in isolation an error will be returned. It is preferably called on the results from debris_nc or debris_inc function. A graph with horizontal and vertical lines used in separating the populations is returned and if to_retain="refined", a circle made of dashed lines is drawn around Synechococcus cyanobacteria cell population points.


cyanoFilter documentation built on Jan. 9, 2020, 5:08 p.m.