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Trajectory line plots with conditioning

Source: R/trajPlot.R
trajPlot.Rd

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",
  map = TRUE,
  group = NULL,
  cols = "default",
  crs = 4326,
  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 = TRUE,
  key.title = group,
  key.position = "right",
  key.columns = 1,
  strip.position = "top",
  auto.text = TRUE,
  plot = TRUE,
  ...
)

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

type determines how the data are split, i.e., conditioned, and then plotted. The default is will produce a single plot using the entire data. Type can be one of the built-in types as detailed in cutData e.g. "season", "year", "weekday" and so on. For example, type = "season" will produce four plots — one for each season.

It is also possible to choose type as another variable in the data frame. If that variable is numeric, then the data will be split into four quantiles (if possible) and labelled accordingly. If type is an existing character or factor variable, then those categories/levels will be used directly. This offers great flexibility for understanding the variation of different variables and how they depend on one another.

type can be up length two e.g. type = c("season", "weekday") will produce a 2x2 plot split by season and day of the week. Note, when two types are provided the first forms the columns and the second the rows.

map

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

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 for plotting. Passed to openColours().

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.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

Should a key be drawn? Defaults to TRUE.

key.title

The title of the key.

key.position

Location where the scale key should be plotted. Allowed arguments currently include "top", "right", "bottom", and "left".

key.columns

Number of columns to be used in the key.

strip.position

Location where the facet 'strips' are located when using type. When one type is provided, can be one of "left", "right", "bottom" or "top". When two types are provided, this argument defines whether the strips are "switched" and can take either "x", "y", or "both". For example, "x" will switch the 'top' strip locations to the bottom of the plot.

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.

plot

Should a plot be produced? FALSE can be useful when analysing data to extract plot components and plotting them in other ways.

...

Addition options are passed on to cutData() for type handling. Some additional arguments are also available:

  • xlab, ylab and main override the x-axis label, y-axis label, and plot title.

  • layout sets the layout of facets - e.g., layout(2, 5) will have 2 columns and 5 rows.

  • fontsize overrides the overall font size of the plot.

  • border sets the border colour of each bar.

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.

See also

Other trajectory analysis functions: importTraj(), trajCluster(), trajLevel()

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,
  lwd = 2,
  cex = 4
)
} # }