aRchi (version 2.1.3)

plot,aRchi,ANY-method: Plot an object of class aRchi

Description

Plot an object of class aRchi.

Usage

# S4 method for aRchi,ANY
plot(
  x,
  y,
  transparency = 1,
  color = "white",
  bg = "black",
  lwd = 3,
  show_point_cloud = FALSE,
  skeleton = TRUE,
  leaves = FALSE,
  lit = TRUE
)

Arguments

x

An aRchi object

y

Unused (inherited from R base)

transparency

The transparency of the cylinders

color

The color of the cylinders. Can be either a single color or a level of organization: "branching_order" for branching branching_order, "cylinder" to coloryze each cylinder independently, "segment" to coloryze the branch segments, "axis" to coloryze the axis, "A0" to colorize only the main axis from Compute_A0 function

bg

The background color

lwd

line width of the skeleton

show_point_cloud

logical (Default = FALSE). Display the point cloud ?

skeleton

logical (Default is TRUE). Display the skeleton only (i.e segments). Faster than displaying the whole QSM with the fleshed cylinders.

leaves

logical (Default is FALSE). Display the leaves ?

lit

logical (Default is TRUE). Specify if lighting calculation should take place on the geometry. Only applies if skeleton = FALSE.

Details

Plot an object of class aRchi in a 3d device. The QSM can be plotted according to different level of organization and the point cloud can be displayed if available.

Examples

# \donttest{
# Read an aRchi file with at least a QSM
file=system.file("extdata","Tree_1_aRchi.aRchi",package = "aRchi")
Tree1_aRchi=read_aRchi(file)
# Plot the QSM by coloring the branching order
plot(Tree1_aRchi,color="branching_order")
# Same with the fleshed cylinder and the point cloud
plot(Tree1_aRchi,color="branching_order",skeleton=FALSE,show_point_cloud=TRUE)
# }