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Plot QSM

Source: R/plot_qsm.R
plot_qsm.Rd

Efficiently plot QSMs and point clouds. Uses the Rcpp and RGL libraries as backends.

Usage

plot_qsm(
  cylinder = NULL,
  radius = NULL,
  color = NULL,
  palette = NULL,
  alpha = 1,
  facets = 6,
  skeleton = FALSE,
  skeleton_lwd = NULL,
  cloud = NULL,
  pt_color = NULL,
  pt_size = NULL,
  triangulation = NULL,
  tri_color = NULL,
  tri_palette = NULL,
  axes = TRUE,
  axes_color = NULL,
  grid = FALSE,
  grid_color = NULL,
  hover = FALSE,
  bg_color = NULL,
  lit = TRUE,
  pan = TRUE,
  normalize = FALSE
)

Arguments

cylinder

A QSM cylinder data frame.

radius

Radius column name either quoted or unquoted. Defaults to the modified radii.

color

Optional cylinder color parameter. Colors must be a single hex color string, a grDevices::colors(), a vector of hex colors, or a quoted/unquoted column name. It can also be set to "random" to generate a random solid color, or FALSE to disable color on export. Vectors must have the same length as the cylinder data frame.

palette

Optional 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.

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, but can be increased to improve visual smoothness at the cost of 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 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. Accepts hex colors, grDevices::colors(), or "random". Defaults to black.

pt_size

Size of the points. Defaults to 0.1.

triangulation

Plot the stem triangulation mesh from TreeQSM. Defaults to NULL.

tri_color

Color of the triangulation mesh. Colors must be a single hex color.

tri_palette

Optional triangulation color palette for z values. Supports the same inputs as palettes.

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 TRUE. Can be set to FALSE.

pan

Use right mouse button to pan plot. Defaults to TRUE, but is disabled when hover is enabled.

normalize

Normalize the QSM to 0,0,0 based on the provided data. Defaults to FALSE.

Value

A rgl plot

Examples


## TreeQSM Processing Chain & Triangulation
file <- system.file("extdata/QSM.mat", package = "rTwig")
qsm <- import_qsm(file)
#> Importing TreeQSM
cylinder <- qsm$cylinder
cylinder <- update_cylinders(cylinder)
#> Updating Cylinder Ordering
#> Calculating Total Children
#> Building Cylinder Network
#> Caching Network
#> Verifying Topology
#> Calculating Growth Length
#> Calculating Reverse Branch Order
#> Calculating Branch Segments
#> Calculating Alternate Branch Numbers
#> Calculating Path Metrics
plot_qsm(cylinder)
#> Plotting Cylinders
#> Panning plot on rgl device: 1

triangulation <- qsm$triangulation
plot_qsm(triangulation = triangulation)
#> Plotting Triangulation
#> Panning plot on rgl device: 1