plot_qsm function

Plot QSM

Efficiently plot QSMs, point clouds, leaves, and stem triangulation meshes. Plots can be combined and extensively customized.

plot_qsm(
  cylinder = NULL,
  radius = NULL,
  color = NULL,
  palette = NULL,
  alpha = 1,
  facets = 6,
  skeleton = FALSE,
  skeleton_lwd = 1,
  cloud = NULL,
  pt_color = "#000000",
  pt_palette = NULL,
  pt_size = NULL,
  pt_alpha = 1,
  triangulation = NULL,
  tri_color = NULL,
  tri_palette = NULL,
  tri_alpha = 1,
  leaves = NULL,
  lf_color = "#5BA803",
  lf_alpha = 1,
  axes = TRUE,
  axes_color = "#000000",
  grid = FALSE,
  grid_color = "#D3D3D3",
  hover = FALSE,
  bg_color = "#FFFFFF",
  lit = FALSE,
  pan = TRUE,
  normalize = FALSE,
  mesh = NULL
)

Arguments

• cylinder: QSM cylinder data frame.
• radius: Radius column name either quoted or unquoted. Defaults to the modified radii.
• color: Optional cylinder color parameter. color must be a single hex color string, a grDevices::colors(), a vector of hex colors, or a quoted/unquoted column name. Vectors must have the same length as the cylinder data frame. color = "random" will generate a random color applied to all cylinders. Defaults to branching order.
• palette: Optional cylinder color palette for numerical data. Palettes include colourvalues::color_palettes() or a user supplied RGB palette matrix with the length of cylinder. It can also be set to "random" to generate a random palette. If combined with color = "random", each cylinder will have a random, distinct color.
• alpha: Set the transparency of the cylinders. Defaults to 1. 1 is opaque and 0 is fully transparent.
• facets: The number of facets in the polygon cross section. Defaults to 6. A higher number of facets improves visual smoothness at the cost of plotting speed, performance and memory.
• skeleton: Plot the QSM skeleton instead of cylinders. Defaults to FALSE.
• skeleton_lwd: Skeleton line width. Defaults to 1.
• cloud: Point cloud data frame or matrix where the first three columns are the x, y, and z coordinates.
• pt_color: Optional point cloud color parameter. pt_color must be a single hex color string, a grDevices::colors(), a vector of hex colors, or a quoted/unquoted column name. pt_color = "random" will generate a random color for all points. Vectors must have the same length as the point cloud data frame.
• pt_palette: Optional point cloud color palette for numerical data. pt_palette includes colourvalues::color_palettes() or a user supplied RGB palette matrix with the length of the points. It can also be set to "random" to generate a random palette. If combined with color = "random", each point will have a random, distinct color.
• pt_size: Size of the points. Defaults to 0.1.
• pt_alpha: Set the transparency of the point cloud. Defaults to 1. 1 is opaque and 0 is fully transparent.
• triangulation: Stem triangulation mesh from TreeQSM. Defaults to NULL.
• tri_color: Color of the triangulation mesh. Accepts hex colors, grDevices::colors(), or "random". Defaults to rainbow z-axis.
• tri_palette: Optional triangulation color palette for z values. Supports the same inputs as palette.
• tri_alpha: Set the transparency of the triangulation mesh. Defaults to 1. 1 is opaque and 0 is fully transparent.
• leaves: Leaf mesh in the rgl::mesh3d() format. Defaults to NULL.
• lf_color: Color of the leaves. Defaults to leaf green. Accepts hex colors, grDevices::colors(),"random", or "random_vertex". lf_color = "random" assigns a random color to all leaves, while lf_color = "random_vertex" which assigns a random color to each vertex.
• lf_alpha: Set the transparency of the leaves. Defaults to 1. 1 is opaque and 0 is fully transparent.
• axes: Show plot axes. Defaults to TRUE.
• axes_color: Set the axes color. Defaults to black.
• grid: Show plot grid lines. Defaults to FALSE.
• grid_color: Set grid lines color. Defaults to grey.
• hover: Show cylinder and branch id on mouse hover. Defaults to FALSE.
• bg_color: Set the background color of the plot. Accepts hex colors or grDevices::colors(). Defaults to white.
• lit: Enable light source in plot. Defaults to FALSE.
• pan: Use right mouse button to pan the plot. Defaults to TRUE. Panning is disabled when hover = TRUE.
• normalize: Normalize the cylinders to 0,0,0. Defaults to FALSE.
• mesh: Plot any rgl::mesh3d() object.

Returns

An rgl::open3d() plot

Examples

## TreeQSM
file <- system.file("extdata/QSM.mat", package = "rTwig")
qsm <- import_treeqsm(file)
cylinder <- qsm$cylinder
cylinder <- update_cylinders(cylinder)
plot_qsm(cylinder)

triangulation <- qsm$triangulation
plot_qsm(triangulation = triangulation)