- mydata
A data frame containing at least two numeric variables to plot.
- x
Name of the x-variable to plot. Note that x can be a date field or a
factor. For example, x can be one of the openair built in
types such as "year" or "season".
- y
Name of the numeric y-variable to plot.
- z
Name of the numeric z-variable to plot for method = "scatter"
or method = "level". Note that for method = "scatter" points
will be coloured according to a continuous colour scale, whereas for
method = "level" the surface is coloured.
- method
Methods include “scatter” (conventional scatter plot),
“hexbin” (hexagonal binning using the hexbin package).
“level” for a binned or smooth surface plot and “density” (2D
kernel density estimates).
- group
The grouping variable to use, if any. Setting this to a variable
in the data frame has the effect of plotting several series in the same
panel using different symbols/colours etc. If set to a variable that is a
character or factor, those categories or factor levels will be used
directly. If set to a numeric variable, it will split that variable in to
quantiles.
- avg.time
This defines the time period to average to. Can be
“sec”, “min”, “hour”, “day”, “DSTday”,
“week”, “month”, “quarter” or “year”. For much
increased flexibility a number can precede these options followed by a
space. For example, a timeAverage of 2 months would be period = "2
month". See function timeAverage for further details on this. This
option se useful as one method by which the number of points plotted is
reduced i.e. by choosing a longer averaging time.
- data.thresh
The data capture threshold to use (\
the data using avg.time. A value of zero means that all available
data will be used in a particular period regardless if of the number of
values available. Conversely, a value of 100 will mean that all data will
need to be present for the average to be calculated, else it is recorded as
NA. Not used if avg.time = "default".
- statistic
The statistic to apply when aggregating the data; default is
the mean. Can be one of "mean", "max", "min", "median", "frequency", "sd",
"percentile". Note that "sd" is the standard deviation and "frequency" is
the number (frequency) of valid records in the period. "percentile" is the
percentile level (\
"percentile" option - see below. Not used if avg.time = "default".
- percentile
The percentile level in percent used when statistic =
"percentile" and when aggregating the data with avg.time. The
default is 95. Not used if avg.time = "default".
- 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.
- smooth
A smooth line is fitted to the data if TRUE; optionally
with 95 percent confidence intervals shown. For method = "level" a
smooth surface will be fitted to binned data.
- spline
A smooth spline is fitted to the data if TRUE. This is
particularly useful when there are fewer data points or when a connection
line between a sequence of points is required.
- linear
A linear model is fitted to the data if TRUE; optionally
with 95 percent confidence intervals shown. The equation of the line and R2
value is also shown.
- ci
Should the confidence intervals for the smooth/linear fit be shown?
- mod.line
If TRUE three lines are added to the scatter plot to
help inform model evaluation. The 1:1 line is solid and the 1:0.5 and 1:2
lines are dashed. Together these lines help show how close a group of
points are to a 1:1 relationship and also show the points that are within a
factor of two (FAC2). mod.line is appropriately transformed when x
or y axes are on a log scale.
- cols
Colours to be used for plotting. Options include
“default”, “increment”, “heat”, “jet” and
RColorBrewer colours --- see the openair openColours
function for more details. For user defined the user can supply a list of
colour names recognised by R (type colours() to see the full list).
An example would be cols = c("yellow", "green", "blue")
- plot.type
lattice plot type. Can be “p” (points ---
default), “l” (lines) or “b” (lines and points).
- key
Should a key be drawn? The default is TRUE.
- key.title
The title of the key (if used).
- key.columns
Number of columns to be used in the key. With many
pollutants a single column can make to key too wide. The user can thus
choose to use several columns by setting columns to be less than the
number of pollutants.
- key.position
Location where the scale key is to plotted. Allowed
arguments currently include “top”, “right”, “bottom”
and “left”.
- strip
Should a strip be drawn? The default is TRUE.
- log.x
Should the x-axis appear on a log scale? The default is
FALSE. If TRUE a well-formatted log10 scale is used. This can
be useful for checking linearity once logged.
- log.y
Should the y-axis appear on a log scale? The default is
FALSE. If TRUE a well-formatted log10 scale is used. This can
be useful for checking linearity once logged.
- x.inc
The x-interval to be used for binning data when method =
"level".
- y.inc
The y-interval to be used for binning data when method =
"level".
- limits
For method = "level" the function does its best to
choose sensible limits automatically. However, there are circumstances when
the user will wish to set different ones. The limits are set in the form
c(lower, upper), so limits = c(0, 100) would force the plot
limits to span 0-100.
- windflow
This option allows a scatter plot to show the wind
speed/direction shows as an arrow. The option is a list e.g. windflow
= list(col = "grey", lwd = 2, scale = 0.1). This option requires wind
speed (ws) and wind direction (wd) to be available.
The maximum length of the arrow plotted is a fraction of the plot dimension
with the longest arrow being scale of the plot x-y dimension. Note,
if the plot size is adjusted manually by the user it should be re-plotted
to ensure the correct wind angle. The list may contain other options to
panel.arrows in the lattice package. Other useful options
include length, which controls the length of the arrow head and
angle, which controls the angle of the arrow head.
This option works best where there are not too many data to ensure
over-plotting does not become a problem.
- y.relation
This determines how the y-axis scale is plotted.
“same” ensures all panels use the same scale and “free” will
use panel-specific scales. The latter is a useful setting when plotting
data with very different values.
- x.relation
This determines how the x-axis scale is plotted.
“same” ensures all panels use the same scale and “free” will
use panel-specific scales. The latter is a useful setting when plotting
data with very different values.
- ref.x
See ref.y for details.
- ref.y
A list with details of the horizontal lines to be added
representing reference line(s). For example, ref.y = list(h = 50, lty
= 5) will add a dashed horizontal line at 50. Several lines can be plotted
e.g. ref.y = list(h = c(50, 100), lty = c(1, 5), col = c("green",
"blue")). See panel.abline in the lattice package for more
details on adding/controlling lines.
- k
Smoothing parameter supplied to gam for fitting a smooth
surface when method = "level".
- dist
When plotting smooth surfaces (method = "level" and
smooth = TRUE, dist controls how far from the original data
the predictions should be made. See exclude.too.far from the
mgcv package. Data are first transformed to a unit square. Values
should be between 0 and 1.
- map
Should a base map be drawn? This option is under development.
- 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.
- ...
Other graphical parameters are passed onto cutData and an
appropriate lattice plot function (xyplot, levelplot
or hexbinplot depending on method). For example,
scatterPlot passes the option hemisphere = "southern" on to
cutData to provide southern (rather than default northern)
hemisphere handling of type = "season". Similarly, for the default
case method = "scatter" common axis and title labelling options
(such as xlab, ylab, main) are passed to xyplot
via quickText to handle routine formatting. Other common graphical
parameters, e.g. layout for panel arrangement, pch for plot
symbol and lwd and lty for line width and type, as also
available (see examples below).
For method = "hexbin" it can be useful to transform the scale if it
is dominated by a few very high values. This is possible by supplying two
functions: one that that applies the transformation and the other that
inverses it. For log scaling (the default) for example, trans =
function(x) log(x) and inv = function(x) exp(x). For a square root
transform use trans = sqrt and inv = function(x) x^2. To not
carry out any transformation the options trans = NULL and inv
= NULL should be used.