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# Function to create a plot for the spatstat class ‘fv’, combined with 'Quantum Plots' from: | |
# Esser, D. S., Leveau, J. H. J., Meyer, K. M., & Wiegand, K. (2014). Spatial scales of interactions among bacteria and between bacteria and the leaf surface. FEMS Microbiology Ecology, 91(3), fiu034. http://doi.org/10.1093/femsec/fiu034 | |
# The colored bands highlight the spatial scales at which the summary statistics deviate from the simulation envelopes. | |
quantumPlot <- function(x,colour=c("#d73027", "#ffffbf", "#91bfdb")){ | |
# load Packages | |
require(ggplot2) | |
require(ggthemes) | |
# convert fv to dataframe | |
env.data <- as.data.frame(tree.data) | |
env.data <- env.data[-1,] | |
# plot it | |
gg_quantomPlot <- ggplot(env.data, aes(r, obs))+ | |
# plot observed value | |
geom_line(colour=c("#4d4d4d"))+ | |
# plot simulation envelopes | |
geom_ribbon(aes(ymin=lo,ymax=hi),alpha=0.1, colour=c("#e0e0e0")) + | |
# axes names and limits | |
ylim(min(env.data$obs)-1, max(env.data$obs)+2) + | |
xlab("Distance r (m)") + | |
ylab("summary statistic") + | |
# plot expected value, according to null model | |
geom_hline(yintercept=1, linetype = "dashed", colour=c("#999999")) + | |
# plot 'Quantums' | |
geom_rug(data=env.data[env.data$obs > env.data$hi,], sides="b", colour=colour[1]) + | |
geom_rug(data=env.data[env.data$obs < env.data$lo,], sides="b", colour=colour[2]) + | |
geom_rug(data=env.data[env.data$obs >= env.data$lo & env.data$obs <= env.data$hi,], sides="b", color=colour[3]) + | |
# make it look beautiful | |
theme_tufte() | |
return(gg_quantomPlot) | |
} | |
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