plotGCaMP_multi: plotGCaMP_multi

Description Usage Arguments Examples

View source: R/plotGCaMP_multi.R

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

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plotGCaMP_multi(FileFilter, matlab = FALSE, genotype, cue = cue,
  food = OP50, startPulse = 29.5, endPulse = 59.5,
  center_on_pulse = FALSE, show.plots = TRUE, use.Fmax = FALSE,
  neuron = GCAMP, linear = FALSE, nls = TRUE, backsub = FALSE,
  plot.raw = FALSE, heatmap_limits = "auto", folderPath, ...)

Arguments

FileFilter

string to search/subset filenames

matlab

whether to use matfiles or data from ImageJ quantification. Defaults to TRUE (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 amplitude to 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

plot.raw

do you want to use raw deltaF/F values - ie not exponentially corrected? Defaults to FALSE

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

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

mikeod38/MF.matR documentation built on Feb. 3, 2019, 1:54 a.m.