plotSpatial {scalpel} | R Documentation |
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:
|
neuronSet |
Which set of neurons should be plotted:
use |
neuronsToDisplay |
Vector giving which neurons' spatial components to plot. The indices refer to which columns to plot
of |
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 |
videoHeight |
The height of the video (in pixels). This only needs to be specified if the user is plotting |
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)