plotResults: Plot both the spatial and temporal components from Step 3 of...
In scalpel: Processes Calcium Imaging Data

Description Usage Arguments Details Value See Also Examples

We plot the temporal components, displaying the estimated fluorescence over time for each spatial component, along with a map of the spatial components.

plotResults(
  scalpelOutput,
  neuronsToDisplay = NULL,
  colVec = NULL,
  titleA = "",
  titleZ = "",
  ylabZ = "",
  fileName = NULL,
  pctTransp = 0.7,
  number = TRUE,
  border = FALSE
)

`scalpelOutput`	An object returned by one of the SCALPEL functions: `scalpel` or `scalpelStep3`.
`neuronsToDisplay`	Vector giving which neurons' spatial and temporal components to plot. The indices refer to which columns of `scalpelOutput$Afilter` to plot. 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.
`titleA`	Label for the title of the spatial components plot.
`titleZ`	Label for the title of the temporal components plot.
`ylabZ`	Label for the y-axis of the temporal components plot.
`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.
`border`	Logical value indicating whether only the borders of the neurons should be plotted.

If lambdaIndex is NULL, each temporal component is scaled by its largest value. If lambdaIndex is specified, each temporal component is scaled by its largest value across all of the lambda values. Temporal components that were zeroed out in the sparse group lasso are omitted from the plot, and their corresponding spatial components are shown in gray.

None

scalpelStep3, scalpel, plotSpatial, plotTemporal

## 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:
plotResults(scalpelOutput = scalpelOutput)

#example with optional parameters:
#plot only two of the neurons, do not number neurons, draw the outlines of the neurons
plotResults(scalpelOutput = scalpelOutput, neuronsToDisplay = c(1,2),
           number = FALSE, border = TRUE)

## End(Not run)