plotGCaMP_multi: plotGCaMP_multi

In mikeod38/MF.matR: Takes mirofluidics data and does stuff with it

plotGCaMP_multi

Description

Function is a wrapper for exp.fit.all.log.lin which outputs corrected GCaMP signals as well as plots showing original and corrected signals. Also plots average trace for GCaMP signal. Inputs are matfiles with a "signal" field, or .csv files from imageJ analysis. The script searches recursively for matfiles (*.mat) or csv files (\*.csv) from a file (can be any placeholder file). Need to exclude matfiles that are not GCaMP files either using FileFilter, or by putting only relevant files in the folder. Default startpulse assumes 400ms delay for camera recording. Requires max_delta helper function time etc...

Usage

plotGCaMP_multi(
  FileFilter,
  matlab = FALSE,
  genotype = genotype,
  cue = cue,
  food = OP50,
  startPulse = 29.5,
  endPulse = 59.5,
  center_on_pulse = "none",
  show.plots = TRUE,
  use.Fmax = FALSE,
  neuron = GCAMP,
  linear = FALSE,
  nls = TRUE,
  backsub = FALSE,
  exp.fit = FALSE,
  heatmap_limits = "auto",
  folderPath,
  ...
)

Arguments

FileFilter	string to search/subset filenames
matlab	whether to use matfiles or data from ImageJ quantification. Defaults to FALSE (matfiles)
genotype	label the genotype for these data
cue	label the stimulus cue.
food	label to food cue
startPulse	begin of stimulus
endPulse	endPulse time of stimulus
center_on_pulse	optional parameter to center delF values by the mean of the stimulus duration 'OFF' = Bring values to mean delF of 2nd half of pulse duration, order by OFF responses 'ON' = Bring values to mean delF of 2nd half pre-pulse duration, order by ON responses
show.plots	render plots for baseline correction - defaults to TRUE
use.Fmax	normalize all amplitudes to within 0-1
neuron	neuron being analyzed
linear	optional argument piped into exp.fit.all.log.lin include a linear term in the fit?
backsub	do you want to subtract background ie subtract ROI of background from the mean cell ROI? Defaults to TRUE
exp.fit	do you want to use raw deltaF/F values - ie exponentially corrected? Defaults to TRUE, which means it will be corrected
heatmap_limits	optional 3-value vector defining the color scale and y axis limits, ie c(-1,0,2)
folderpath	user supplied path for recursive file search. If missing, it will prompt for a fiel selection.

Examples

data <- plotGCaMP_multi(N2, genotype = N2, cue = octanol)

mikeod38/MF.matR documentation built on Feb. 3, 2023, 6:23 p.m.