plot.vpts {bioRad}R Documentation

Plot a time series of vertical profiles (vpts)

Description

Plot a time series of vertical profiles of class vpts.

Usage

## S3 method for class 'vpts'
plot(
  x,
  xlab = "time",
  ylab = "height [m]",
  quantity = "dens",
  log = NA,
  barbs = TRUE,
  barbs_height = 10,
  barbs_time = 20,
  barbs_dens_min = 5,
  zlim,
  legend_ticks,
  legend.ticks,
  main,
  barbs.h = 10,
  barbs.t = 20,
  barbs.dens = 5,
  na_color = "#C8C8C8",
  nan_color = "white",
  n_color = 1000,
  palette = NA,
  ...
)

Arguments

x

A vp class object inheriting from class vpts.

xlab

A title for the x-axis.

ylab

A title for the y-axis.

quantity

Character string with the quantity to plot, one of 'dens','eta','dbz','DBZH' for density, reflectivity, reflectivity factor and total reflectivity factor, respectively.

log

Logical, whether to display quantity data on a logarithmic scale.

barbs

Logical, whether to overlay speed barbs.

barbs_height

Integer, number of barbs to plot in altitudinal dimension.

barbs_time

Integer, number of barbs to plot in temporal dimension.

barbs_dens_min

Numeric, lower threshold in aerial density of individuals for plotting speed barbs in individuals/km^3.

zlim

Optional numerical atomic vector of length 2, specifying the range of quantity values to plot.

legend_ticks

Numeric atomic vector specifying the ticks on the color bar.

legend.ticks

Deprecated argument, use legend_ticks instead.

main

A title for the plot.

barbs.h

Deprecated argument, use barbs_height instead.

barbs.t

Deprecated argument, use barbs_time instead.

barbs.dens

Deprecated argument, use barbs_dens_min instead.

na_color

Color to use for NA values, see class vpts() conventions.

nan_color

Color to use for NaN values, see class vpts() conventions.

n_color

The number of colors (>=1) to be in the palette.

palette

(Optional) character vector of hexadecimal color values defining the plot color scale, e.g. output from viridis

...

Additional arguments to be passed to the low level image plotting function.

Details

Aerial abundances can be visualized in four related quantities, as specified by argument quantity:

Aerial velocities can be visualized in three related quantities, as specified by argument quantity:

barbs

In the speed barbs, each half flag represents 2.5 m/s, each full flag 5 m/s, each pennant (triangle) 25 m/s

legend_ticks / zlim

Default legend ticks and plotting range are specified based on quantity, radar wavelength (S- vs C-band), and value of log

log

Quantities u and v cannot be plotted on a logarithmic scale, because these quantities assume negative values. For quantities DBZH and dbz log=TRUE is ignored, because these quantities are already logarithmic.

Value

No return value, side effect is a plot.

Examples

# locate example file:
ts <- example_vpts
# plot density of individuals for the first 500 time steps, in the altitude
# layer 0-3000 m.
plot(ts[1:500], ylim = c(0, 3000))
# plot total reflectivity factor (rain, birds, insects together):
plot(ts[1:500], ylim = c(0, 3000), quantity = "DBZH")
# regularize the time grid, which includes empty (NA) profiles at
# time steps without data:
ts_regular <- regularize_vpts(ts)
plot(ts_regular)
# change the color of missing NA data to red
plot(ts_regular, na_color="red")
# change the color palette:
plot(ts_regular[1:1000], ylim = c(0, 3000), palette=viridis::viridis(1000))
# change and inverse the color palette:
plot(ts_regular[1:1000], ylim = c(0, 3000), palette=rev(viridis::viridis(1000, option="A")))
# plot the speed profile:
plot(ts_regular[1:1000], quantity="ff")
# plot the northward speed component:
plot(ts_regular[1:1000], quantity="v")
# plot speed profile with more legend ticks,
plot(ts_regular[1:1000], quantity="ff", legend_ticks=seq(0,20,2), zlim=c(0,20))

[Package bioRad version 0.7.3 Index]