This function takes in a flowframe with debris removed and identifies Synechococcus cyanobacteria cell population in the provided frame.
bs4_nc(bs4bs5, p1, p2, others, to_retain = c("refined", "potential"))flowframe with debris (left) removed.
first flowcytometer channel that can be used to separate cells of interest from the rest, e.g. "RED.B.HLin".
second flowcytometer channel that can be used to separate cells of interest from the rest, e.g. "YEL.B.HLin"
row numbers for non-debris events. This is provided by the
debris_nc or debris_inc function.
should potential candidates be retained or further gating be applied to filter out only certain Synechococcus cyanobacteria cells.
list containing;
syn_reduced - flowframe containing only Synechococcus cyanobacteria cells
others_nk - unidentified particle positions
syn_pos - Synechococcus cyanobacteria cells positions
others_nk2 - other unidentified particle positions
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.