| muscle.plot.multi {GoodFibes} | R Documentation |
Plot multi muscle fibers with a muscle outline
Description
Uses functions from rgl to plot all fibers (smoothed with splines) in a fiber list. Also uses grayscale values from the image stack to determine the external boundaries of the muscle based on concave hulls. Boundaries are plotted as a series of single outlines sampled across the image.
Usage
muscle.plot.multi(fiber.list, images, df = 2, outline = 30,
cols = NULL, mirror.axis = FALSE)
Arguments
fiber.list |
A list of fibers with $fiber points. Generated by good.fibes or processed cleaned by other functions |
images |
A character vector of image stack file names. Generated with list.files |
df |
The degrees of freedom to pass to splines2::nsp for smoothing fiber paths. df = 1 gives a straight path, while >1 gives increasingly curved paths |
outline |
The number of wireframe "outlines" to draw the muscle boundaries |
cols |
An optional vector of colors, the same order and length of fiber.list |
mirror.axis |
Depending on the way the image stack was exported, fibers may be reflected from their original original. mirror.axis = TRUE will reflect the fibers before plotting to correct this |
Value
Returns a 3D plot
Author(s)
J. Arbour
References
Arbour, J. In Prep. GoodFibes: an R package for the detection of muscle fibers from diceCT scans.
See Also
Examples
olddir<-getwd()
#### this downloads the ant dataset image stack
#### if you have it already downloaded you can navigate to that folder
setwd(tempdir())
download.file(url=
"https://github.com/jessica-arbour/Ant-Muscle-Image-Stack/raw/main/Ant_data.zip",
destfile="antdata.zip")
unzip("antdata.zip")
setwd(paste0(getwd(),"/Ant data"))
####
images<-list.files(pattern=".png")
data(ant.final)
muscle.plot.multi(ant.final, images, df=1, mirror.axis = TRUE)
setwd(olddir)