Plot QSM

Plots QSM cylinders and point clouds using the rgl library

Usage

plot_qsm(
  cylinder,
  radius = NULL,
  color = NULL,
  palette = NULL,
  facets = 6,
  cloud = NULL,
  pt_color = NULL,
  pt_size = NULL,
  axes = TRUE,
  hover = FALSE,
  skeleton = FALSE,
  bg_color = NULL
)

Arguments

cylinder

QSM cylinder data frame

radius

Column name of radii as a quoted string. Defaults to the modified radii.

color

Optional cylinder color parameter. Colors must be a single hex color, a vector of hex colors, or a quoted column name. It can also be set to "random" to generate a random solid color. Vectors must have the same length as the cylinder data frame.

palette

Optional color palette for numerical data. Palettes include: viridis, inferno, plasma, magma, cividis, and rainbow.

facets

The number of facets in the polygon cross section. Defaults to 6, but can be increased to improve visual smoothness at the cost of performance and memory.

cloud

Point cloud data frame where the first three columns are the x, y, and z coordinates in the same coordinate system as the QSM. Defaults to NULL.

pt_color

Color of the point cloud. Defaults to black. Can be set to "random".

pt_size

Size of the points. Defaults to 0.1.

axes

Show plot axes. Defaults to TRUE.

hover

Show cylinder and branch id on mouse hover. Defaults to FALSE.

skeleton

Plot the QSM skeleton instead of cylinders. Defaults to FALSE.

bg_color

Set the background color of the rgl plot. Defaults to NULL.

Value

A rgl plot

Examples

## TreeQSM Processing Chain
file <- system.file("extdata/QSM.mat", package = "rTwig")
qsm <- import_qsm(file)
#> Importing TreeQSM .mat
cylinder <- qsm$cylinder
cylinder <- update_cylinders(cylinder)
#> Updating Cylinder Ordering
#> Calculating Total Children
#> Building Cylinder Network
#> Verifying Topology
#> Calculating Growth Length
#> Calculating Reverse Branch Order
#> Calculating Branch Segments
#> Calculating Alternate Branch Numbers
#> Calculating Distance From Base
#> Calculating Average Distance To Twigs
plot_qsm(cylinder)
#> Plotting QSM
#> Plotting Cylinders

## SimpleForest Processing Chain
file <- system.file("extdata/QSM.csv", package = "rTwig")
cylinder2 <- read.csv(file)
cylinder2 <- update_cylinders(cylinder2)
#> Updating Branch Ordering
#> Calculating Total Children
#> Building Cylinder Network
#> Verifying Topology
#> Calculating Distance From Base
#> Calculating Average Distance To Twigs
plot_qsm(cylinder2)
#> Plotting QSM
#> Plotting Cylinders

## All Parameters
file2 <- system.file("extdata/cloud.txt", package = "rTwig")
cloud <- read.table(file2, header = FALSE)

plot_qsm(
  cylinder,
  radius = "UnmodRadius",
  color = "growthLength",
  palette = "viridis",
  facets = 100,
  cloud = cloud,
  pt_color = "random",
  pt_size = 1,
  axes = FALSE,
  hover = TRUE,
  bg_color = "black"
)
#> Plotting QSM
#> Plotting Cylinders
#> Plotting Cloud