plotSpatial: Plot spatial components from Steps 2 or 3 of SCALPEL.
In scalpel: Processes Calcium Imaging Data

Description Usage Arguments Details Value See Also Examples

We plot the dictionary elements obtained from Step 2 of SCALPEL, or the filtered dictionary elements from Step 3 of SCALPEL.

plotSpatial(
  scalpelOutput = NULL,
  neuronSet = "",
  neuronsToDisplay = NULL,
  colVec = NULL,
  title = "",
  fileName = NULL,
  pctTransp = 0.7,
  number = TRUE,
  addToPlot = FALSE,
  border = FALSE,
  zoom = FALSE,
  A = NULL,
  videoHeight = NULL
)

`scalpelOutput`	An object returned by one of these SCALPEL functions: `scalpel`, `scalpelStep2`, or `scalpelStep3`.
`neuronSet`	Which set of neurons should be plotted: use `"A"` for the dictionary elements resulting from `scalpelStep2` and saved as `scalpelOutput$A`, or use `"Afilter"` for the filtered dictionary elements resulting from `scalpelStep3` and saved as `scalpelOutput$Afilter`.
`neuronsToDisplay`	Vector giving which neurons' spatial components to plot. The indices refer to which columns to plot of `scalpelOutput$Afilter` (if `neuronSet="Afilter"`), or `scalpelOutput$A` (if `neuronSet="A"`). By default, all components are plotted. Users may also specify `"kept"`, which will exclude all dictionary elements discarded using a previous call to `reviewNeurons` or `reviewNeuronsInteractive`.
`colVec`	Vector of colors to use, which are chosen automatically if the default value of NULL is used.
`title`	Label for the title.
`fileName`	If provided, the plot will be saved to the specified location.
`pctTransp`	The percent transparency (in [0,1]) for the colors used to plot the neurons. The default value is 0.7.
`number`	Logical value indicating whether the neurons should be numbered.
`addToPlot`	Logical value indicating whether these neurons should be plotted to an existing plot.
`border`	Logical value indicating whether only the borders of the neurons should be plotted.
`zoom`	Logical value indicating whether the plot should be zoomed in to exclude any area not containing neurons.
`A`	Optional advanced user argument: A matrix containing the spatial components to plot, where the ith column of `A` is a vector of 1's and 0's, indicating whether each pixel is contained in the ith spatial component. By default, this argument is ignored and the dictionary elements saved in `scalpelOutput$A` or `scalpelOutput$Afilter` are plotted. If `A` is provided, `scalpelOutput` will be ignored and `neuronsToDisplay` will refer to the columns of `A`.
`videoHeight`	The height of the video (in pixels). This only needs to be specified if the user is plotting `A`.

When neuronSet="Afilter", spatial components corresponding to temporal components that were zeroed out in the sparse group lasso are plotted in gray, unless colVec is specified by the user.

None

scalpelStep2, scalpelStep3, scalpel, plotResults

## 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:
plotSpatial(scalpelOutput = scalpelOutput, neuronSet = "Afilter")

#example with optional parameters:
#plot only two of the neurons, add a title, do not number neurons,
#and draw the outlines of the neurons
plotSpatial(scalpelOutput = scalpelOutput, neuronsToDisplay = c(1,2), neuronSet = "Afilter",
           title = "First two neurons", number = FALSE, border = TRUE)

## End(Not run)