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Create a simple Time-of-Day plot of light logger data, faceted by Date

Source: R/gg_day.r
gg_day.Rd

gg_day() will create a simple ggplot for every data in a dataset. The result can further be manipulated like any ggplot. This will be sensible to refine styling or guides.

Usage

gg_day(
  dataset,
  start.date = NULL,
  end.date = NULL,
  x.axis = Datetime,
  y.axis = MEDI,
  aes_col = NULL,
  aes_fill = NULL,
  group = Id,
  geom = "point",
  scales = c("fixed", "free_x", "free_y", "free"),
  x.axis.breaks = hms::hms(hours = seq(0, 24, by = 3)),
  y.axis.breaks = c(-10^(5:0), 0, 10^(0:5)),
  y.scale = "symlog",
  y.scale.sc = FALSE,
  x.axis.label = "Time of Day",
  y.axis.label = "Illuminance (lx, MEDI)",
  format.day = "%d/%m",
  title = NULL,
  subtitle = NULL,
  interactive = FALSE,
  facetting = TRUE,
  jco_color = TRUE,
  ...
)

Arguments

dataset

A light logger dataset. Expects a dataframe. If not imported by LightLogR, take care to choose a sensible variable for the x.axis..

start.date, end.date

Choose an optional start or end date within your dataset. Expects a date, which can also be a character that is interpretable as a date, e.g., "2023-06-03". If you need a Datetime or want to cut specific times of each day, use the filter_Datetime() function. Defaults to NULL, which means that the plot starts/ends with the earliest/latest date within the dataset.

x.axis, y.axis

column name that contains the datetime (x, defaults to "Datetime" which is automatically correct for data imported with LightLogR) and the dependent variable (y, defaults to "MEDI", or melanopic EDI, which is a standard measure of stimulus strength for the nonvisual effects of light). Expects a symbol. Needs to be part of the dataset.

aes_col, aes_fill

optional arguments that define separate sets and colors or fills them. Expects anything that works with the layer data ggplot2::aes(). The default color palette can be overwritten outside the function (see examples).

group

Optional column name that defines separate sets. Useful for certain geoms like boxplot.Expects anything that works with the layer data ggplot2::aes()

geom

What geom should be used for visualization? Expects a character

scales

For ggplot2::facet_wrap(), should scales be "fixed", "free" or free in one dimension ("free_y" is the default). Expects a character.

x.axis.breaks, y.axis.breaks

Where should breaks occur on the x and y.axis? Expects a numeric vector with all the breaks. If you want to activate the default behaviour of ggplot2, you need to put in ggplot2::waiver().

y.scale

How should the y-axis be scaled?

  • Defaults to "symlog", which is a logarithmic scale that can also handle negative values.

  • "log10" would be a straight logarithmic scale, but cannot handle negative values.

  • "identity" does nothing (continuous scaling).

  • a transforming function, such as symlog_trans() or scales::identity_trans(), which allow for more control.

y.scale.sc

logical for whether scientific notation shall be used. Defaults to FALSE.

x.axis.label, y.axis.label

labels for the x- and y-axis. Expects a character.

format.day

Label for each day. Default is %d/%m, which shows the day and month. Expects a character. For an overview of sensible options look at base::strptime()

title

Plot title. Expects a character.

subtitle

Plot subtitle. Expects a character.

interactive

Should the plot be interactive? Expects a logical. Defaults to FALSE.

facetting

Should an automated facet by day be applied? Default is TRUE and uses the Day.data variable that the function also creates if not present.

jco_color

Should the ggsci::scale_color_jco() color palette be used? Defaults to TRUE.

...

Other options that get passed to the main geom function. Can be used to adjust to adjust size, linewidth, or linetype.

Value

A ggplot object

Details

Besides plotting, the function creates two new variables from the given Datetime:

  • Day.data is a factor that is used for facetting with ggplot2::facet_wrap(). Make sure to use this variable, if you change the faceting manually. Also, the function checks, whether this variable already exists. If it does, it will only convert it to a factor and do the faceting on that variable.

  • Time.data is an hms created with hms::as_hms() that is used for the x.axis

The default scaling of the y-axis is a symlog scale, which is a logarithmic scale that only starts scaling after a given threshold (default = 0). This enables values of 0 in the plot, which are common in light logger data, and even enables negative values, which might be sensible for non-light data. See symlog_trans() for details on tweaking this scale. The scale can also be changed to a normal or logarithmic scale - see the y.scale argument for more.

The default scaling of the color and fill scales is discrete, with the ggsci::scale_color_jco() and ggsci::scale_fill_jco() scales. To use a continuous scale, use the jco_color = FALSE setting. Both fill and color aesthetics are set to NULL by default. For most geoms, this is not important, but geoms that automatically use those aesthetics (like geom_bin2d, where fill = stat(count)) are affected by this. Manually adding the required aesthetic (like aes_fill = ggplot2::stat(count) will fix this).

Examples

#use `col`for separation of different sets
plot <- gg_day(
sample.data.environment,
scales = "fixed",
end.date = "2023-08-16",
y.axis.label = "mEDI (lx)",
aes_col = Id)
#> Only Dates will be used from start.date and end.date input. If you also want to set Datetimes or Times, consider using the `filter_Datetime()` function instead.
plot


#you can easily overwrite the color scale afterwards
plot + ggplot2::scale_color_discrete()
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.


#or change the facetting
plot + ggplot2::facet_wrap(~Day.data + Id)