plotResultsAllLambda: Plot both the spatial and temporal components for the...

In scalpel: Processes Calcium Imaging Data

Description

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

Usage

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

Arguments

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.
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.

Details

Temporal components that were zeroed out in the sparse group lasso and their corresponding spatial components are shown in gray for both plots.

Value

None

See Also

scalpelStep3, scalpel, plotSpatial, plotTemporal

Examples

## 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:
plotResultsAllLambda(scalpelOutput = scalpelOutput)

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

## End(Not run)

scalpel documentation built on Feb. 3, 2021, 9:05 a.m.