plot_qsm {rTwig} | R Documentation |
Plot QSM
Description
Plots QSM cylinders using the rgl library
Usage
plot_qsm(
cylinder,
radius = NULL,
cyl_color = NULL,
cyl_palette = NULL,
cyl_sides = 8,
cloud = NULL,
pt_color = NULL,
pt_size = NULL,
axes = TRUE,
hover = FALSE
)
Arguments
cylinder |
QSM cylinder data frame |
radius |
Vector of cylinder radii. Defaults to modified cylinders from the cylinder data frame. |
cyl_color |
Optional cylinder color parameter. Colors must be a single hex color, or a vector or column of hex colors with the same length as the cylinder data frame. |
cyl_palette |
Optional color palette for numerical data. Palettes include: viridis, inferno, plasma, magma, cividis, and rainbow. |
cyl_sides |
The number of sides in the polygon cross section. Defaults to 8, but can be increased to improve visual smoothness. |
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. |
pt_color |
Color of the point cloud. Defaults to black. |
pt_size |
Size of the points as a number. Defaults to 0.1. |
axes |
Show plot axes. Defaults to TRUE. |
hover |
Show cylinder ID and branch on mouse hover. Defaults to FALSE. |
Value
A rgl QSM plot
Examples
## TreeQSM Processing Chain
file <- system.file("extdata/QSM.mat", package = "rTwig")
qsm <- import_qsm(file)
cylinder <- qsm$cylinder
cylinder <- update_cylinders(cylinder)
cylinder <- correct_radii(cylinder, twigRad = 4.23)
plot_qsm(cylinder)
## SimpleForest Processing Chain
file <- system.file("extdata/QSM.csv", package = "rTwig")
cylinder2 <- read.csv(file)
cylinder2 <- update_cylinders(cylinder2)
cylinder2 <- correct_radii(cylinder2, twigRad = 4.23)
plot_qsm(cylinder2)
## All Parameters
file2 <- system.file("extdata/cloud.txt", package = "rTwig")
cloud <- read.table(file2, header = FALSE)
plot_qsm(
cylinder,
radius = cylinder$UnmodRadius,
cyl_color = cylinder$GrowthLength,
cyl_palette = "viridis",
cyl_sides = 100,
cloud = cloud,
pt_color = "white",
pt_size = 1,
axes = FALSE,
hover = TRUE
)