lcd: Liquid Crystal Diagram (LCD) plot

In cj-holmes/gglcd:

Description

lcd() is a wrapper for gglcd::geom_lc(). It produces simple LC alignmnet diagrams using ggplot2.

Usage

lcd(
  angle_b = 0,
  angle_t = 90,
  angle_function = NULL,
  angle_n = 0,
  n_mol_x = 30,
  n_mol_y = 30,
  x_jitter = 0.4,
  y_jitter = 0.4,
  lc_length = 0.05,
  lc_width = 0.016,
  diagram_aspect = 1,
  seed = NULL,
  surface_b = NULL,
  surface_t = NULL,
  lc_shape = "rectangle",
  ellipse_res = 35,
  return_df = FALSE,
  themeing = TRUE,
  show_function = FALSE,
  lc_lwd = 0.2,
  surface_b_lwd = 0.2,
  surface_t_lwd = 0.2,
  bg_lwd = 0.2,
  lc_fill = "grey80",
  lc_col = "black",
  bg_fill = "white",
  bg_col = "black",
  surface_b_fill = "black",
  surface_b_col = NA,
  surface_t_fill = "black",
  surface_t_col = NA
)

Arguments

angle_b	Angle of molecules at bottom of plot (degrees, measured anti-clockwise from +ve x)
angle_t	Angle of molecules at top of plot (degrees, measured anti-clockwise from +ve x)
angle_function	A function that takes a value of the image height (from 0 to 1) and returns the angle of a molecule at that height
angle_n	Noise to be added to angles (a random angle from -angle_n:angle_n is added to each molecule)
n_mol_x	Number of molecules in x (default is 30)
n_mol_y	Number of molecules in y (default is 30)
x_jitter	Jitter to apply to molecule centres in x. Value is applied as a proportion of lc_length (default = 0.4)
y_jitter	Jitter to apply to molecule centres in y. Value is applied as a proportion of lc_length (default = 0.4)
lc_length	Length of LC molecule (vector of length 1 or (n_mol_x * n_mol_y))
lc_width	Width of LC molecule (vector of length 1 or (n_mol_x * n_mol_y))
diagram_aspect	Aspect ratio of diagram (length / width)
seed	Random seed for reproducability
surface_b	Height of bottom surface layer
surface_t	Height of top surface layer
lc_shape	One of "rectangle" (default) or "ellipse"
ellipse_res	Resolution of ellipse polygons
return_df	Should just the dataframe be returned (Default: FALSE)
themeing	Should themeing be applied (Default: TRUE)
show_function	Logical. Print functional form of angle_function over diagram
lc_lwd	Linewidth of LC molecules
surface_b_lwd	Linewidth of bottom surface
surface_t_lwd	Linewidth of top surface
bg_lwd	Linewidth of plot border
lc_fill	Fill colour for LC molecules
lc_col	Border colour for LC molecules
bg_fill	Fill colour for diagram background
bg_col	Line colour for diagram background
surface_b_fill	Fill colour of bottom surface
surface_b_col	Line colour of bottom surface
surface_t_fill	Fill colour of top surface
surface_t_col	Line colour of top surface

Examples

lcd(0, 360)
lcd(0, 360, return_df = TRUE)

cj-holmes/gglcd documentation built on July 30, 2020, 9:54 a.m.