plot_qsm: Plot QSM

In rTwig: Realistic Quantitative Structure Models

Plot QSM

Description

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)
cylinder <- qsm$cylinder
cylinder <- update_cylinders(cylinder)
plot_qsm(cylinder)

## SimpleForest Processing Chain
file <- system.file("extdata/QSM.csv", package = "rTwig")
cylinder2 <- read.csv(file)
cylinder2 <- update_cylinders(cylinder2)
plot_qsm(cylinder2)

## 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"
)

rTwig documentation built on Sept. 11, 2024, 7:01 p.m.