View source: R/plotting_tools.R
Plot a BNPR output
1 2 3 4 5 6 7 8 | plot_BNPR(BNPR_out, traj = NULL, xlim = NULL, ylim = NULL,
nbreaks = 40, lty = 1, lwd = 2, col = "black", main = "",
log = "y", ylab = "Effective Population Size", xlab = "Time",
xmarline = 3, axlabs = NULL, traj_lty = 2, traj_lwd = 2,
traj_col = col, newplot = TRUE, credible_region = TRUE,
heatmaps = TRUE, heatmap_labels = TRUE,
heatmap_labels_side = "right", heatmap_labels_cex = 0.7,
heatmap_width = 7, yscale = 1, ...)
|
BNPR_out |
output of BNPR or BNPR_PS. |
traj |
function summarizing the true effective population size trajectory. |
xlim |
numeric x-axis interval. |
ylim |
numeric y-axis interval. |
nbreaks |
integer number of bins for sampling heatmap. |
lty |
line type for estimated trajectory. |
lwd |
line width for estimated trajectory. |
col |
color for estimated trajectory. |
main |
character main plot title. |
log |
character which axes to plot log-scale. Defaults to "y". |
ylab |
character y-axis label. |
xlab |
character x-axis label. |
xmarline |
numeric if not using default x-axis labels, how far to put the labels from the axis. |
axlabs |
character vector x-axis labels. |
traj_lty, traj_lwd, traj_col |
line type, line width, and line color for the true trajectory. |
newplot |
boolean whether to create a new plot or superimpose over a previously open plot. |
credible_region |
logical whether to display pointwise credible region. |
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_labels_cex |
numeric scaling factor for heatmap labels. |
heatmap_width |
numeric how wide heatmaps should be. |
yscale |
numeric scaling applied to all effective population calculations. |
... |
additional arguments to be passed onto plot(). |
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