POPdemog (version 1.0.3)

PlotMig: Plot migration event(s) at a particular time

Description

This function plots migration events at a particular time point based on the output of PlotMS with demo.out = T and plot.out = F. The time_pt or event determines the time points that are plotted. The add and map.pos parameters allow the migration graph to be added to other backgrounds such as maps.

Usage

PlotMig(time_pt = NULL, event = 1, mig_par, demograph_out,
  size.scale = mig_par$size.scale, time.scale = mig_par$time.scale,
  linear.scale = mig_par$linear.scale, log.base = mig_par$log.base,
  col.pop = mig_par$col.pop, col.arrow = mig_par$col.arrow,
  xlim = mig_par$xlim, ylim = mig_par$ylim, lwd.arrow = mig_par$lwd.arrow,
  length.arrowtip = mig_par$length.arrowtip,
  angle.arrowtip = mig_par$angle.arrowtip, toposize.scale = 1,
  add = FALSE, map.pos = NULL, m.adjust = 0)

Arguments

time_pt

A numeric value defining the time point for the migrations which will be plotted. time_pt should be in the scale defined by time.scale. For example, time_pt = 3 when time.scale = "log10year" corresponds to the migrations 10^3 years ago.

event

An index to define at which time to plot migration(s). Every demographic event has an index in the order of time. Demographic changes at the same time are all defined as the same event and share the same index.

mig_par

A list contained all settings for plotting the demographic graph, see PlotMS.

demograph_out

A list containing all demographic information, see PlotMS.

size.scale

A keyword to define the scaling of lineage width. "topology" returns only topology structure among simulated populations, ignoring both the population sizes and the length of time between any demographic events. "linear" linearly scales the lineage widths as a function of the population size, with the scale factor defined by the variable linear.scale; "log" scales the lineage width logarithmically as a function of the population size. The logarithm base is defined by the variable log.base.

time.scale

A keyword to define the time scale used in the plot. It can be "4Ne", "generation", "year", "kyear", and "log10year". When the size.scale = "topology", this parameter will be ignored.

linear.scale

Linear scale magnitude, to be applied when size.scale = "linear".

log.base

The base of logarithm, to be applied when size.scale = "log".

col.pop

Population lineage color.

col.arrow

Migration arrow color.

xlim

The range of x-axis.

ylim

The range of y-axis.

lwd.arrow

Control the line width of arrow representing a migration. The arrow width is defined by 0.5+migration strength*lwd.arrow.

length.arrowtip

Length of the edges of the arrow tip.

angle.arrowtip

The angle of the arrow tip, between 0 and 90.

toposize.scale

Control the scaling of the size of circle when the size.scale = "topology".

add

A logical value allowing one to add the migrations to another background (2-D only). Positions for every population dime should be defined in map.pos.

map.pos

A matrix with two columns, the ith row is the coordinate for the ith population.

m.adjust

Migration threshold for plotting migration events. Migration events with strength higher than m.adjust will be shown. The migration strength is defined as the proportion of the target population being replaced by the source population per generation. Default value is 0.

See Also

PlotMS

Examples

# NOT RUN {
test.mig.cmd <- "./ms 15 100 -t 3.0 -I 6 0 7 0 0 8 0 -m 1 2 2.5 -m 2 1 2.5 
-m 2 3 2.5 -m 3 2 2.5 -m 4 5 2.5 -m 5 4 2.5 -m 5 6 2.5 -m 6 5 2.5 
-em 2.0 3 4 2.5 -em 2.0 4 3 2.5"
out <- PlotMS(input.cmd = test.mig.cmd, type = "ms", 
N4 = 10000, plot.out = FALSE, demo.out = TRUE);
#check all migration events
events <- out$mig_par$events
print(events)
#check the time for those migration events
timeofevents <- out$mig_par$time[events]
print(timeofevents)
#plot event by event
par(mfrow = c(1, 2))
PlotMig(event = 1, demograph_out = out$demograph_out, mig_par = out$mig_par)
title("Event-1");
PlotMig(event = 2, demograph_out = out$demograph_out, mig_par = out$mig_par, 
col.pop = 1:6, xlim = c(-5,4))
title("Event-2", cex.main = 3);
legend("topleft", col = 1:6, pch = 20, bty = "n", cex = 2,
legend = c("pop-1", "pop-2", "pop-3", "pop-4", "pop-5", "pop-6"))
# }