View source: R/plotting_tools.R
Plot seasonal overlays
1 2 3 4 5 6 7 8 | plot_seasonality_beast(BEAST_out, zero_date, start = 0, years = NULL,
period = 1, ylim = NULL, nbreaks = 40, lty = 1, lwd = 2,
col_years = "gray", col_median = "black", main = "",
axlabs = NULL, xlab = "Time", xmarline = 1,
ylab = "Effective Population Size", log_y = TRUE,
samp_times = NULL, n_sampled = NULL, heatmaps = TRUE,
heatmap_labels = TRUE, heatmap_labels_side = "right",
heatmap_width = 7, legend = NULL, yscale = 1, ...)
|
BEAST_out |
list containing 'midpts', 'medianEffPop', 'q975EffPop', and 'q025EffPop'. |
zero_date |
numeric date (in decimal years) representing 't=0' in 'BEAST_out' |
start |
numeric value between 0 and 'period' controlling the right side of the plot. |
years |
numeric how many years or periods to overlay. |
period |
numeric representing how long one year or other seasonal period is in the units of 'BEAST_out'. |
ylim |
numeric y-axis interval. |
nbreaks |
integer number of bins in the sampling time histogram heatmap. |
lty |
numeric line type. |
lwd |
numeric line width. |
col_years |
color of individual trajectory |
col_median |
color of the median estimate. |
main |
character main figure title. |
axlabs |
character vector x-axis labels. |
xlab |
character x-axis label. |
xmarline |
numeric if not using default x-axis labels, how far to put the labels from the axis. |
ylab |
character y-axis label. |
log_y |
logical whether to log-scale the y-axis. |
samp_times |
numeric vector of sampling times. |
n_sampled |
integer vector of number of samples taken at each element of samp_times. |
heatmaps |
boolean whether to display sampling and coalescent heatmaps. |
heatmap_labels |
boolean whether to display labels on heatmaps. |
heatmap_labels_side |
string which side of plot to display heatmaps. |
heatmap_width |
numeric vertical width of sampling time histogram heatmap. |
legend |
character legend text. The defauly, NULL, disables. |
yscale |
numeric scaling applied to all effective population calculations. |
... |
additional arguments to be passed onto plot(). |
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