plotVideoVariance {scalpel} | R Documentation |
Plot a summary of the fluorescence in the video.
Description
We plot a heat map of the variance of each pixel across the frames.
Usage
plotVideoVariance(
scalpelOutput,
neuronSet = "",
videoType = "processed",
neuronsToOutline = "all",
shrinkLargest = FALSE,
shrinkQuantile = 0.95,
title = "",
Y = NULL
)
Arguments
scalpelOutput |
An object returned by one of the SCALPEL functions:
|
neuronSet |
This argument is ignored unless the class of |
videoType |
Specify whether to plot the processed data from Step 0 (default; |
neuronsToOutline |
Specify whether to plot outlines of all neurons (default; |
shrinkLargest |
Logical value indicating whether the values above |
shrinkQuantile |
The quantile value above which pixel values will be shrunk. By default, this is the 95th quantile. |
title |
Label for the title. |
Y |
An object of class |
Value
None
See Also
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:
plotVideoVariance(scalpelOutput = scalpelOutput, neuronSet = "Afilter")
#example with optional parameters:
#previous showed summary of processed data,
#can instead show raw data, not outline the neurons found, and add a title
plotVideoVariance(scalpelOutput = scalpelOutput, videoType = "raw",
neuronsToOutline = "none", title = "Raw Data")
#if you have video data read in already using 'getY' function, you can provide it
rawY = getY(scalpelOutput = scalpelOutput, videoType = "raw")
plotVideoVariance(scalpelOutput = scalpelOutput, neuronSet = "Afilter", Y = rawY)
## End(Not run)