shift.dot.ggplot {AlleleShift} | R Documentation |
Shifts of Allele Frequencies as Response to Climate Change
Description
The function shows changes in allele frequencies between the baseline and future/past climate.
Usage
shift.dot.ggplot(freq.future,
mean.change = FALSE, change.FUN = stats::median,
baseline.colour = "black",
future.colour = "dodgerblue3",
manual.colour.values=c("firebrick3", "chartreuse4"))
Arguments
freq.future |
Result from |
mean.change |
Aggregate changes among alleles. |
change.FUN |
Function used the aggregate changes. |
baseline.colour , future.colour , manual.colour.values |
Colours to be used in the plots. |
Value
The function generates a ggplot that depicts changes between baseline and future/past allele frequencies of the populations.
Author(s)
Roeland Kindt (World Agroforestry, CIFOR-ICRAF)
See Also
shift.pie.ggplot
, shift.moon.ggplot
, shift.waffle.ggplot
, shift.surf.ggplot
Examples
# The data can be obtained via the count.model and freq.model calibrations.
# These procedures are not repeated here.
data(Poptri.freq.future)
ggdot1 <- shift.dot.ggplot(Poptri.freq.future)
ggdot1
# create an animation
## Not run:
library(ggplot2)
library(gganimate)
library(gifski)
# The data is an interpolation and extrapolation between the baseline and future climate.
# For actual application, interpolate between climate data from available sources
data(Poptri.1985to2085)
ggdot.all <- ggplot(data=Poptri.1985to2085, group=Decade) +
scale_y_continuous(limits=c(-0.1, 1.1),
breaks=c(0.0, 0.25, 0.5, 0.75, 1.0)) +
geom_errorbar(aes(x=Pop, ymin=LCL, ymax=UCL),
colour="grey30", width=0.8, show.legend=FALSE) +
geom_segment(aes(x=Pop, y=Allele.freq, xend=Pop, yend=Freq.e2, colour=increasing),
size=1.2) +
geom_point(aes(x=Pop, y=Allele.freq),
colour="black", size=10, alpha=0.7) +
geom_point(aes(x=Pop, y=Freq.e2),
colour="dodgerblue3", size=10, alpha=0.7) +
coord_flip() +
xlab(element_blank()) +
ylab("Allele frequencies") +
theme(panel.grid.minor = element_blank()) +
labs(colour="Future change in allele frequencies") +
scale_colour_manual(values=c("firebrick3", "chartreuse4"),
labels=c("decreasing", "increasing")) +
theme(axis.text.x=element_text(angle=90, vjust=0.5, size=10)) +
theme(legend.position="top") +
facet_grid( ~ Allele, scales="free")
ggdot.all
ggdot.anim <- ggdot.all +
transition_states(as.factor(Decade), transition_length = 10, state_length = 100) +
labs(title = "Decade: {closest_state}s")
ggdot.anim2 <- animate(ggdot.anim, fps=5, width=1280, height=720)
getwd()
anim_save(filename="Allele shift animation.gif", animation=ggdot.anim2)
## End(Not run)
[Package AlleleShift version 1.1-2 Index]