shift.moon.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.moon.ggplot(baseline.moon, future.moon,
manual.colour.values = c("white", "grey", "firebrick3", "chartreuse4"),
manual.colour.codes = c("A baseline ", "B", "A decreasing", "A increasing"))
moon.waxer(freq.in, sort.index= "Pop.index",
mean.change = FALSE, change.FUN = stats::median,
freq.focus = "Allele.freq",
ypos = 0, right = TRUE)
Arguments
baseline.moon , future.moon |
Result from |
manual.colour.values |
Colours to be used in the plot. |
manual.colour.codes |
Sequence for the manual colour values. |
freq.in |
Result from |
sort.index |
Sequence of the populations in the plot. |
mean.change |
Aggregate changes among alleles. |
change.FUN |
Function used the aggregate changes. |
freq.focus |
Allele frequency for which to calculate statistics, either 'Allele.freq' or 'Freq.e2'. |
ypos , right |
Arguments used for plotting, mainly as in |
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.dot.ggplot
, shift.pie.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.baseline)
data(Poptri.freq.future)
Poptri.baseline.moon <- moon.waxer(Poptri.freq.baseline,
sort.index="Latitude.index")
Poptri.future.moon <- moon.waxer(Poptri.freq.future,
sort.index="Latitude.index",
freq.focus="Freq.e2",
ypos=1)
ggmoon1 <- shift.moon.ggplot(Poptri.baseline.moon,
Poptri.future.moon)
ggmoon1
[Package AlleleShift version 1.1-2 Index]