## ---- setup,echo=FALSE ---------------
library(cda)
library(rgl)
library(dielectric)
library(ggplot2)
library(reshape2)
library(plyr)
theme_set(theme_bw() + theme(strip.background=element_blank()))
## ---- demo ---------------
wvl <- seq(400, 700)
gold <- epsAu(wvl)
ar <- 2
N <- 5
cl <- cluster_helix(N, R0=12, pitch=15,
delta=pi/2, delta0=0, right=TRUE,
a=5/ar, b=5/ar, c=5,
angles="helix")
simulation <- function(N=3, scale=1, ar=1, ...){
cl <- cluster_helix(N, R0=12*scale, pitch=15*scale,
delta=pi/2, delta0=0, right=TRUE,
a=5/ar*scale, b=5/ar*scale, c=5*scale,
angles="helix")
spectrum_oa(cl, material = gold, medium=1.33)
}
params <- expand.grid(N=seq(3, 7), ar= c(1, 1.1))
comparison <- mdply(params, simulation, .progress = "text")
## ---- plot,echo=TRUE,fig.width=8 ---------------
symmetrise_scale <- function(p, axis = c("y", "x"), facet = "dichroism"){
axis <- match.arg(axis)
gb <- ggplot_build(p)
layout <- gb$layout$panel_layout
vars <- setdiff(names(layout), c("PANEL", "ROW", "COL", "SCALE_X", "SCALE_Y"))
facets <- layout[,vars]
ranges <- gb$layout$panel_ranges
type <- switch(axis, "x" = "x.range", "y" = "y.range")
lims <- sapply(ranges, "[[", type)
fname <- as.character(vars[1])
lims2 <- as.vector(t(tcrossprod(apply(abs(lims), 2, max), c(-1,1))))
dummy <- setNames(data.frame(rep(facets, each=2), lims2), c(fname, axis))
if("type" %in% names(dummy))
dummy <- dummy[dummy$type == facet, , drop=FALSE]
switch(axis,
"x" = p + geom_blank(data=dummy, aes(x=x, y=Inf), inherit.aes = FALSE),
"y" = p + geom_blank(data=dummy, aes(x=Inf, y=y), inherit.aes = FALSE))
}
p <-
ggplot(data=subset(comparison, type == "dichroism" & variable == "extinction")) +
facet_wrap(~ ar, scales="free" ,labeller=labeller(.cols=label_both)) +
geom_line(aes(wavelength, value/N,
colour=factor(N))) +
labs(y=expression(sigma[ext]*" /"*nm^2),
x=expression(wavelength*" /"*nm), colour="# particles")
symmetrise_scale(p)
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