plotCandidateFrame {scalpel}

Plot preliminary dictionary element from Step 1 of SCALPEL and its corresponding frame.

Description

We plot the specified preliminary dictionary element, along with the frame of Y from which the component was derived in Step 1 of SCALPEL.

Usage

plotCandidateFrame(
  scalpelOutput,
  AzeroIndex = NULL,
  AIndex = NULL,
  AfilterIndex = NULL,
  member = NULL,
  videoType = "processed",
  shrinkLargest = FALSE,
  shrinkCutoff = NULL,
  Y = NULL
)

Arguments

scalpelOutput

An object returned by one of the SCALPEL functions: scalpel, scalpelStep1, scalpelStep2, or scalpelStep3.

AzeroIndex

The preliminary dictionary element of interest. The index refers to the column of scalpelOutput$Azero. Specify only one of the following: AzeroIndex, AIndex, or AfilterIndex.

AIndex

The dictionary element (i.e., cluster) of interest. The index refers to the column of scalpelOutput$A. Note that the class of scalpelOutput must be scalpel, scalpelStep2, or scalpelStep3 if specifying AIndex, and member must also be specified. Specify only one of the following: AzeroIndex, AIndex, or AfilterIndex.

AfilterIndex

The sparse group lasso component of interest. The index refers to the column of scalpelOutput$Afilter. Note that the class of scalpelOutput must be scalpel or scalpelStep3 if specifying AfilterIndex, and member must also be specified. Specify only one of the following: AzeroIndex, AIndex, or AfilterIndex.

member

Which member of the cluster corresponding to AIndex or AfilterIndex to plot. Ignored if AzeroIndex is specified.

videoType

Specify whether to plot the processed data from Step 0 (default; videoType="processed") or raw data (videoType="raw"). This is ignored if Y is provided.

shrinkLargest

Logical value indicating whether the values above shrinkCutoff should be shrunk when plotting. Shrinking these values allows us to better visualize the areas with the largest fluorescence.

shrinkCutoff

The value above which pixel values will be shrunk. By default, this will be chosen as min(scalpelOutput$thresholdVec).

Y

An object of class scalpelY, which results from running the getY function. When not specified, Y is automatically read in, but specifying Y is recommended when the user would like to call this function many times, as this avoids reading the video into memory repeatedly.

Value

None

See Also

scalpelStep1, scalpel

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:
plotCandidateFrame(scalpelOutput = scalpelOutput, AzeroIndex = 10)

#example with optional parameters:
#plot raw data instead of processed
plotCandidateFrame(scalpelOutput = scalpelOutput, AzeroIndex = 10, videoType = "raw")

#same plot but if you have video data read in already
#using 'getY' function, you can provide it
rawY = getY(scalpelOutput = scalpelOutput, videoType = "raw")
plotCandidateFrame(scalpelOutput = scalpelOutput, AzeroIndex = 10, Y = rawY)

## End(Not run)