geom_flame: Create 'flame' polygons.

Description

This function will create polygons between two lines. If given a temperature and theshold time series, like that produced by detect_event, the output will meet the specifications of Hobday et al. (2016) shown as 'flame polygons.' If one wishes to plot polygons below a given threshold, and not above, switch the values being fed to the y and y2 aesthetics. This function differs in use from event_line in that it must be created as a ggplot 'geom' object. The benefit of this being that one may add additional information to the figure as geom layers to ggplot2 graphs as may be necessary.

Usage

geom_flame(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  n = 0,
  n_gap = 0,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping

Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data.

stat

The statistical transformation to use on the data for this layer, as a string.

position

Position adjustment, either as a string, or the result of a call to a position adjustment function.

...

other arguments passed on to layer. These are often aesthetics, used to set an aesthetic to a fixed value, like color = "red" or size = 3. They may also be parameters to the paired geom/stat.

The number of steps along the x-axis (i.e. in a daily time series this would be days) required before the area between y and y2 will be filled in. The default of 0 will fill in _all_ of the area between the lines. The standard to match Hobday et al. (2016) is n = 5.

n_gap

The number of steps along the x-axis (i.e. in a daily time series this would be days) within which to allow geom_flame() to connect polygons. This is useful when one wants to not screen out parts of a polygon that dip only briefly below y before coming back up above it. The defauly of 0 will not connect any of the polygons. The standard to match Hobday et al. (2016) is n_gap = 2.

na.rm

If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.

show.legend

Logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Aesthetics

geom_flame understands the following aesthetics (required aesthetics are in bold):

x
y
y2
colour
fill
size
alpha
linetype

References

Hobday, A.J. et al. (2016), A hierarchical approach to defining marine heatwaves, Progress in Oceanography, 141, pp. 227-238, doi: 10.1016/j.pocean.2015.12.014

Examples

Run this code

# NOT RUN {
ts <- ts2clm(sst_WA, climatologyPeriod = c("1983-01-01", "2012-12-31"))
res <- detect_event(ts)
mhw <- res$clim
mhw <- mhw[10580:10690,]

library(ggplot2)

ggplot(mhw, aes(x = t, y = temp)) +
  geom_flame(aes(y2 = thresh)) +
  geom_text(aes(x = as.Date("2011-02-01"), y = 28,
            label = "That's not a heatwave.\nThis, is a heatwave.")) +
  xlab("Date") + ylab(expression(paste("Temperature [", degree, "C]")))

# }