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.
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,
...
)A ggplot object
A light logger dataset. Expects a dataframe. If not imported
by LightLogR, take care to choose a sensible variable for the x.axis..
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.
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.
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).
Optional column name that defines separate sets. Useful for
certain geoms like boxplot.Expects anything that works with the layer
data ggplot2::aes()
What geom should be used for visualization? Expects a character
"point" for ggplot2::geom_point()
"line" for ggplot2::geom_line()
"ribbon" for ggplot2::geom_ribbon()
as the value is just input into the geom_ function from ggplot2, other variants work as well, but are not extensively tested.
For ggplot2::facet_wrap(), should scales be "fixed", "free"
or free in one dimension ("free_y" is the default). Expects a character.
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().
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.
logical for whether scientific notation shall be used.
Defaults to FALSE.
labels for the x- and y-axis. Expects a
character.
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()
Plot title. Expects a character.
Plot subtitle. Expects a character.
Should the plot be interactive? Expects a logical.
Defaults to FALSE.
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.
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.
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).
#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)
plot
#you can easily overwrite the color scale afterwards
plot + ggplot2::scale_color_discrete()
#or change the facetting
plot + ggplot2::facet_wrap(~Day.data + Id)
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