gglcd is a work in progress - it may not be working properly, so use
it at your own risk!
The goal of gglcd is to programmatically create schematic liquid
crystal (LC) alignment diagrams.
gglcd has two features:
- A ggplot2 geom and stat (
geom_lc()andstat_lc()) for fine control - A convenient wrapper function
lcd()for simple alignment diagrams
library(gglcd)
library(tidyverse)For quick LC alignment diagrams you can use lcd() and specify the
bottom and top anlgle arguments. Under the hood, this is creating an
angle_function (the third argument to lcd()) that varies the angle
linearly from the bottom of the diagram to the top of the diagram. Note
that all themeing can be removed by setting themeing = FALSE. Setting
a seed ensures that the same diagram can be recreated.
lcd(45, -45, seed=1)
lcd(45, -45, seed=1, themeing = FALSE)
The vertical y-scale of the plotting area always ranges from 0 to 1 (so
the plotting area always has a height of 1). The width of the diagram
can be varied by specifying the diagram_aspect argument which is
defined as width/length. lcd() returns a ggplot2 object, so further
layers cab be added as normal
lcd(0, 90) +
geom_hline(yintercept = 0.5, col="orange", size=2)+
labs(title = "Title", subtitle = "Subtitle")
There are a whole load of other arguments to lcd() to control the
format of the output
args(lcd)
#> function (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)
#> NULLFor example, the aspect of the diagram can be changed, bounding surfaces applied and colour elements edited.
lcd(0, 360,
diagram_aspect = 2,
surface_b = 0.1, surface_t = 0.05,
bg_fill = "aquamarine", lc_fill="white")
Non-linear changes in angle can also be specified by the
angle_function argument. Here I create a sinusoidally varying angle
between 0.2 and 0.8 (the vertical scale of the plot is always 0 to 1).
x <- seq(0.2,0.8,l=1000)
y <- sin(seq(0,2*pi,l=1000))*90
af <- approxfun(x,y, rule=2)
lcd(angle_function = af, seed=1, show_function = TRUE, angle_n=2)
The lcd() function described above is a wrapper aronud geom_lc() and
stat_lc(). These functions can be used as normal with a call to
ggplot() for full control over the diagram creation, including the
ability to make additional aesthetic mappings.
A particularly useful argument to lcd() is return_df. If set to
TRUE (default is FALSE), a dataframe of the required aesthetic
mappings (x, y, angle, length, width) is returned, rather than a plot.
This is a convenient way to produce a dataframe that can be passed to
ggplot() (example below).
This example also makes use of the ability to map non-required aesthetics. The fill is mapped to angle.
lcd(-180, 180, return_df = T, seed=1) %>%
print() %>% # view dataframe
ggplot(aes(x, y, angle=angle, length=length, width=width))+
geom_lc(aes(fill=angle))+
coord_fixed()+
scale_fill_gradient2()
#> # A tibble: 900 x 5
#> x y width length angle
#> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0.158 -0.0198 0.016 0.05 -180
#> 2 0.177 -0.0182 0.016 0.05 -180
#> 3 0.434 -0.0178 0.016 0.05 -180
#> 4 0.702 -0.0171 0.016 0.05 -180
#> 5 0.536 -0.0170 0.016 0.05 -180
#> 6 0.601 -0.0164 0.016 0.05 -180
#> 7 0.398 -0.0156 0.016 0.05 -180
#> 8 0.0930 -0.0147 0.016 0.05 -180
#> 9 0.776 -0.0139 0.016 0.05 -180
#> 10 0.268 -0.0136 0.016 0.05 -180
#> # ... with 890 more rows
As length is a required aesthetic for geom_lc(), it can be varied per
LC molecule. Here I have created a function that returns the length as a
function of the position in y for the ‘twist’ category (approximating
the projection of the rotated molecule onto the x-y plane). This is then
mutated onto the dataframe before plotting.
# Define inputs
lc_length <- 0.05
lc_width <- lc_length/3
# Approximate the length projection on to the x-y plane
twist_proj <- approxfun(seq(0,1,l=1000), cos(seq(0, pi/2, l=1000))*lc_length)
bind_rows(
lcd(50, -50, lc_length=lc_length, lc_width=lc_width, return_df = TRUE) %>% mutate(label = "Splay"),
lcd(50, 130, lc_length=lc_length, lc_width=lc_width, return_df = TRUE) %>% mutate(label = "Bend"),
lcd(0, 0, lc_length = lc_length, lc_width=lc_width, return_df = TRUE) %>%
mutate(length = twist_proj(y),
length = case_when(length < lc_width ~ lc_width,
TRUE ~ length),
label = "Twist")
) %>%
ggplot(aes(x, y, angle=angle, length=length, width=width))+
geom_lc()+
facet_wrap(~label)+
coord_fixed()+
theme(legend.position = "none")
If using the lc_shape = 'ellipse' option, a further argument
ellipse_res can be used to control the number of equally spaced points
(in angle) that make up each individual ellipse. The default is
ellipse_res = 35
tibble(x=0.5, y=0.5, angle=45, length=1, width=1/4) %>%
ggplot(aes(x, y, angle=angle, length=length, width=width))+
geom_polygon(stat="lc", aes(col="rectangle"), fill=NA, size=1)+
geom_polygon(stat="lc", lc_shape='ellipse', ellipse_res = 60, aes(col="ellipse_res = 60"), fill=NA, size=1)+
geom_polygon(stat="lc", lc_shape='ellipse', ellipse_res = 35, aes(col="ellipse_res = 35"), fill=NA, size=1)+
geom_polygon(stat="lc", lc_shape='ellipse', ellipse_res = 10, aes(col="ellipse_res = 10"), fill=NA, size=1)+
geom_polygon(stat="lc", lc_shape='ellipse', ellipse_res = 5, aes(col="ellipse_res = 05"), fill=NA, size=1)+
coord_fixed()
With the super useful gganimate package it is also possible to create
custom animations using geom_lc().
