Trajectory line plots with conditioning

This function plots back trajectories. This function requires that data are imported using the importTraj() function, or matches that structure.

Usage

trajPlot(
  mydata,
  lon = "lon",
  lat = "lat",
  pollutant = NULL,
  type = "default",
  group = NULL,
  cols = "default",
  crs = 4326,
  map = TRUE,
  map.res = "medium",
  map.fill = TRUE,
  map.cols = "grey40",
  map.border = "black",
  map.alpha = 0.4,
  map.lwd = 1,
  map.lty = 1,
  grid.col = "deepskyblue",
  grid.nx = 9,
  grid.ny = grid.nx,
  npoints = 12,
  origin = TRUE,
  key.title = group,
  key.position = "right",
  key.columns = 1,
  auto.text = TRUE,
  plot = TRUE,
  key = NULL,
  ...
)

Arguments

mydata

Data frame, the result of importing a trajectory file using importTraj().

lon, lat

Columns containing the decimal longitude and latitude.

pollutant

Pollutant (or any numeric column) to be plotted, if any. Alternatively, use group.

type

Character string(s) defining how data should be split/conditioned before plotting. "default" produces a single panel using the entire dataset. Any other options will split the plot into different panels - a roughly square grid of panels if one type is given, or a 2D matrix of panels if two types are given. type is always passed to cutData(), and can therefore be any of:

A built-in type defined in cutData() (e.g., "season", "year", "weekday", etc.). For example, type = "season" will split the plot into four panels, one for each season.
The name of a numeric column in mydata, which will be split into n.levels quantiles (defaulting to 4).
The name of a character or factor column in mydata, which will be used as-is. Commonly this could be a variable like "site" to ensure data from different monitoring sites are handled and presented separately. It could equally be any arbitrary column created by the user (e.g., whether a nearby possible pollutant source is active or not).

Most openair plotting functions can take two type arguments. If two are given, the first is used for the columns and the second for the rows.

group

A condition to colour the plot by, passed to cutData(). An alternative to pollutant, and used preferentially to pollutant if both are set.

cols

Colours to use for plotting. Can be a pre-set palette (e.g., "turbo", "viridis", "tol", "Dark2", etc.) or a user-defined vector of R colours (e.g., c("yellow", "green", "blue", "black") - see colours() for a full list) or hex-codes (e.g., c("#30123B", "#9CF649", "#7A0403")). Alternatively, can be a list of arguments to control the colour palette more closely (e.g., palette, direction, alpha, etc.). See openColours() and colourOpts() for more details.

crs

The coordinate reference system to use for plotting. Defaults to 4326, which is the WGS84 geographic coordinate system, the standard, unprojected latitude/longitude system used in GPS, Google Earth, and GIS mapping. Other crs values are available - for example, 27700 will use the the OSGB36/British National Grid.

map

Should a base map be drawn? If TRUE the world base map provided by ggplot2::map_data() will be used.

map.res

The scale of the map to use. One of 110, 50, 10 or small, medium, large. Passed to rnaturalearth::ne_countries().

map.fill

Should the base map be a filled polygon? Default is to fill countries.

map.cols

If map.fill = TRUE map.cols controls the fill colour. Examples include map.fill = "grey40" and map.fill = openColours("default", 10). The latter colours the countries and can help differentiate them.

map.border

The colour to use for the map outlines/borders. Defaults to "black".

map.alpha

The transparency level of the filled map which takes values from 0 (full transparency) to 1 (full opacity). Setting it below 1 can help view trajectories, trajectory surfaces etc. and a filled base map.

map.lwd

The map line width, a positive number, defaulting to 1.

map.lty

The map line type. Line types can either be specified as an integer (0 = blank, 1 = solid (default), 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash) or as one of the character strings "blank", "solid", "dashed", "dotted", "dotdash", "longdash", or "twodash", where "blank" uses 'invisible lines' (i.e., does not draw them).

grid.col

The colour of the map grid to be used. To remove the grid set grid.col = "transparent".

grid.nx, grid.ny

The approximate number of ticks to draw on the map grid. grid.nx defaults to 9, and grid.ny defaults to whatever value is passed to grid.nx. Setting both values to 0 will remove the grid entirely. The number of ticks is approximate as this value is passed to scales::breaks_pretty() to determine nice-looking, round breakpoints.

npoints

A dot is placed every npoints along each full trajectory. For hourly back trajectories points are plotted every npoint hours. This helps to understand where the air masses were at particular times and get a feel for the speed of the air (points closer together correspond to slower moving air masses). If npoints = NA then no points are added.

origin

If true a filled circle dot is shown to mark the receptor point.

key.title

Used to set the title of the legend. The legend title is passed to quickText() if auto.text = TRUE.

key.position

Location where the legend is to be placed. Allowed arguments include "top", "right", "bottom", "left" and "none", the last of which removes the legend entirely.

key.columns

Number of columns to be used in a categorical legend. With many categories a single column can make to key too wide. The user can thus choose to use several columns by setting key.columns to be less than the number of categories.

auto.text

Either TRUE (default) or FALSE. If TRUE titles and axis labels will automatically try and format pollutant names and units properly, e.g., by subscripting the "2" in "NO2". Passed to quickText().

plot

When openair plots are created they are automatically printed to the active graphics device. plot = FALSE deactivates this behaviour. This may be useful when the plot data is of more interest, or the plot is required to appear later (e.g., later in a Quarto document, or to be saved to a file).

key

Deprecated; please use key.position. If FALSE, sets key.position to "none".

...

Addition options are passed on to cutData() for type handling. Some additional arguments are also available, varying somewhat in different plotting functions:

title, subtitle, caption, tag, xlab and ylab control the plot title, subtitle, caption, tag, x-axis label and y-axis label, passed to ggplot2::labs() via quickText() if auto.text = TRUE.
xlim, ylim and limits control the limits of the x-axis, y-axis and colorbar scales.
ncol and nrow set the number of columns and rows in a faceted plot.
scales can be "fixed", "free_x", "free_y" or "free" to control whether axes are shared across facets when using type. Also supported are the legacy x.relation and y.relation, which can be either "same" or "free" and get remapped to scales automatically.
Similarly, space, axes, axis.labels, switch and strip.position can be used to customise the appearance of faceted plots. See ggplot2::facet_wrap() and ggplot2::facet_grid() for the arguments these take.
fontsize overrides the overall font size of the plot by setting the text argument of ggplot2::theme(). It may also be applied proportionately to any openair annotations (e.g., N/E/S/W labels on polar coordinate plots).
Various graphical parameters are also supported: linewidth, linetype, shape, size, border, and alpha. Not all parameters apply to all plots. These can take a single value, or a vector of multiple values - e.g., shape = c(1, 2) - which will be recycled to the length of values needed.
lineend, linejoin and linemitre tweak the appearance of line plots; see ggplot2::geom_line() for more information.
In polar coordinate plots, annotate = FALSE will remove the N/E/S/W labels and any other annotations.

Details

Several types of trajectory plot are available:

trajPlot() by default will plot each lat/lon location showing the origin of each trajectory, if no pollutant is supplied.
If a pollutant is given, by merging the trajectory data with concentration data, the trajectories are colour-coded by the concentration of pollutant. With a long time series there can be lots of overplotting making it difficult to gauge the overall concentration pattern. In these cases setting alpha to a low value e.g. 0.1 can help.

The user can also show points instead of lines by plot.type = "p".

Note that trajPlot() will plot only the full length trajectories. This should be remembered when selecting only part of a year to plot.

Author

David Carslaw

Jack Davison

Examples

if (FALSE) { # \dontrun{
# show a simple case with no pollutant i.e. just the trajectories
# let's check to see where the trajectories were coming from when
# Heathrow Airport was closed due to the Icelandic volcanic eruption
# 15--21 April 2010.
# import trajectories for London and plot

lond <- importTraj("london", 2010)

# well, HYSPLIT seems to think there certainly were conditions where trajectories
# orginated from Iceland...
trajPlot(selectByDate(lond, start = "15/4/2010", end = "21/4/2010"))

# plot by day, need a column that makes a date
lond$day <- as.Date(lond$date)
trajPlot(
  selectByDate(lond, start = "15/4/2010", end = "21/4/2010"),
  type = "day"
)

# or show each day grouped by colour, with some other options set
trajPlot(
  selectByDate(lond, start = "15/4/2010", end = "21/4/2010"),
  group = "day",
  cols = "turbo",
  key.position = "right",
  key.columns = 1,
  linewidth = 2,
  size = 4
)
} # }