plotBrightest: Plot the most active frames for a given neuron.
In scalpel: Processes Calcium Imaging Data

Description Usage Arguments Value See Also Examples

For a given neuron, we plot the frames with the highest estimated fluorescence, which results from fitting the sparse group lasso in Step 3 of SCALPEL.

plotBrightest(
  scalpelOutput,
  AfilterIndex,
  videoType = "processed",
  neuronsToOutline = "all",
  brightIndex = 1,
  shrinkLargest = FALSE,
  shrinkCutoff = NULL,
  title = NULL,
  Y = NULL
)

`scalpelOutput`	An object returned by one of the SCALPEL functions: `scalpel` or `scalpelStep3`.
`AfilterIndex`	Scalar giving the neuron for which to plot the brightest frames. The index refers to which column of `scalpelOutput$Afilter` is of interest.
`videoType`	Specify whether to plot the processed data from Step 0 (default; `videoType="processed"`) or raw data (`videoType="raw"`). This is ignored if `Y` is provided.
`neuronsToOutline`	Specify whether to plot outlines of all neurons (default; `neuronsToOutline="all"`), only the outline for `neuron` (`neuronsToOutline="main"`), outlines of only the neurons kept using a previous call to `reviewNeurons` or `reviewNeuronsInteractive` (`neuronsToOutline="kept"`), or none (`neuronsToOutline="none"`).
`brightIndex`	Scalar giving which of the ordered brightest frames to plot. The default is 1, i.e., the brightest frame.
`shrinkLargest`	Logical value indicating whether the values above `shrinkCutoff` should be shrunk when plotting. Shrinking these values allows us to better visualize the areas with the largest fluorescence.
`shrinkCutoff`	The value above which pixel values will be shrunk. By default, this will be chosen as `min(scalpelOutput$thresholdVec)`.
`title`	Label for the title. The default is frame number.
`Y`	An object of class `scalpelY`, which results from running the `getY` function. When not specified, `Y` is automatically read in, but specifying `Y` is recommended when the user would like to call this function many times, as this avoids reading the video into memory repeatedly.

None

scalpel, scalpelStep3

## Not run: 
### many of the functions in this package are interconnected so the
### easiest way to learn to use the package is by working through the vignette,
### which is available at ajpete.com/software

#assumes you have run the example for the "scalpel" function
#simplest example with default parameters:
plotBrightest(scalpelOutput = scalpelOutput, AfilterIndex = 2)

#example with optional parameters:
#only outline neuron corresponding to frame, plot 5th brightest with raw data
plotBrightest(scalpelOutput = scalpelOutput, AfilterIndex = 2, videoType = "raw",
             neuronsToOutline = "main", brightIndex = 5)

#same plot but if you have video data read in already
#using 'getY' function, you can provide it
rawY = getY(scalpelOutput = scalpelOutput, videoType = "raw")
plotBrightest(scalpelOutput = scalpelOutput, AfilterIndex = 2, Y = rawY,
             neuronsToOutline = "main", brightIndex = 5)

## End(Not run)