Package 'plot2'

Add Additional Mapping

Description

This function can be used to adjust the mapping of a plot.

Usage

add_mapping(plot, ...)

Arguments

plot	a ggplot2 plot
...	arguments passed on to ggplot2::aes()

Examples

p <- iris |> plot2(Sepal.Length, Sepal.Width, Species, zoom = TRUE)
p

p |> add_mapping(shape = Species)

---

Add Plot Element

Description

Quickly and conveniently add a new 'geom' to an existing plot2/ggplot model. Like plot2(), these functions support tidy evaluation, meaning that variables can be unquoted. Better yet, they can contain any function with any output length, or any vector. They can be added using the pipe (new base R's ⁠|>⁠ or tidyverse's ⁠%>%⁠).

Usage

add_type(plot, type = NULL, mapping = aes(), ..., data = NULL, move = 0)

add_line(
  plot,
  y = NULL,
  x = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  linetype,
  linewidth,
  ...,
  inherit.aes = NULL,
  move = 0,
  legend.value = NULL
)

add_point(
  plot,
  y = NULL,
  x = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  size,
  shape,
  ...,
  inherit.aes = NULL,
  move = 0,
  legend.value = NULL
)

add_col(
  plot,
  y = NULL,
  x = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  colour_fill,
  width,
  ...,
  inherit.aes = NULL,
  move = 0,
  legend.value = NULL
)

add_errorbar(
  plot,
  min,
  max,
  colour = getOption("plot2.colour", "ggplot2"),
  width = 0.5,
  ...,
  inherit.aes = NULL,
  move = 0
)

add_sf(
  plot,
  sf_data,
  colour = getOption("plot2.colour_sf", "grey50"),
  colour_fill = getOption("plot2.colour_sf_fill", getOption("plot2.colour", "ggplot2")),
  size = 2,
  linewidth = 0.1,
  datalabels = NULL,
  datalabels.colour = "black",
  datalabels.size = 3,
  datalabels.angle = 0,
  datalabels.font = getOption("plot2.font"),
  datalabels.nudge_y = 2500,
  ...,
  inherit.aes = FALSE
)

Arguments

plot	a ggplot2 plot
type	a ggplot2 geom name, all geoms are supported. Full function names can be used (e.g., "geom_line"), but they can also be abbreviated (e.g., "l", "line"). These geoms can be abbreviated by their first character: area ("a"), boxplot ("b"), column ("c"), histogram ("h"), jitter ("j"), line ("l"), point ("p"), ribbon ("r"), violin ("v").
mapping	a mapping created with aes() to pass on to the geom
data	data to use in mapping
move	number of layers to move the newly added geom down, e.g., move = 1 will place the newly added geom down 1 layer, thus directly under the highest layer
x, y	aesthetic arguments
colour, colour_fill	colour of the line or column, will be evaluated with get_colour(). If colour_fill is missing but colour is given, colour_fill will inherit the colour set with colour.
linetype, linewidth, shape, size, width, ...	arguments passed on to the geom
inherit.aes	a logical to indicate whether the default aesthetics should be inherited, rather than combining with them
legend.value	text to show in an additional legend that will be created. Since ggplot2 does not actually support this, it may give some false-positive warnings or messages, such as "Removed 1 row containing missing values or values outside the scale range".
min, max	minimum (lower) and maximum (upper) values of the error bars
sf_data	an 'sf' data.frame
datalabels	a column of sf_data to add as label below the points
datalabels.colour, datalabels.size, datalabels.angle, datalabels.font	properties of datalabels
datalabels.nudge_y	is datalabels is not NULL, the amount of vertical adjustment of the datalabels (positive value: more to the North, negative value: more to the South)

Details

The function add_line() will add:

• geom_hline() if only y is provided;

• geom_vline() if only x is provided;

• geom_line() in all other cases.

The function add_errorbar() only adds error bars to the y values, see Examples.

Value

a ggplot object

Examples

head(iris)
                 
p <- iris |>
  plot2(x = Sepal.Length,
        y = Sepal.Width,
        category = Species,
        zoom = TRUE)
p
  
# if not specifying x or y, current plot data are taken
p |> add_line()
  
# single values for add_line() will plot 'hline' or 'vline'
# even considering the `category` if set
p |> 
  add_line(y = mean(Sepal.Width))

# set `colour` to ignore existing colours
# and use `legend.value` to add a legend
p |> 
  add_line(y = mean(Sepal.Width),
           colour = "red",
           legend.value = "Average")
  
p |> 
  add_line(x = mean(Sepal.Length)) |> 
  add_line(y = mean(Sepal.Width))
  
p |>
  add_point(x = median(Sepal.Length),
            y = median(Sepal.Width),
            shape = 13,
            size = 25,
            show.legend = FALSE)
  
# multiple values will just plot multiple lines
p |> 
  add_line(y = fivenum(Sepal.Width),
           colour = "blue",
           legend.value = "Tukey's Numbers")
  
p |> 
  add_line(y = quantile(Sepal.Width, c(0.25, 0.5, 0.75)),
           colour = c("red", "black", "red"),
           linewidth = 1)
  
# use move to move the new layer down
p |> 
  add_point(size = 5,
            colour = "lightpink",
            move = -1)

# providing x and y will just plot the points as new data,
p |> 
  add_point(y = 2:4,
            x = 5:7,
            colour = "red",
            size = 5)
# even with expanded grid if x and y are not of the same length
p |> 
  add_point(y = 2:4,
            x = 5:8,
            colour = "red",
            size = 5)

# any mathematical transformation of current values is supported
df <- data.frame(var_1 = c(1:100),
                 var_2 = rnorm(100, 100, 25),
                 var_3 = rep(LETTERS[1:5], 5))
df |>
  plot2(var_1, var_2) |> 
  add_line(y = mean(var_2), 
           linetype = 3,
           legend.value = "Average") |>
  add_col(y = var_2 / 5,
          width = 0.25,
          colour = "blue",
          legend.value = "This *is* **some** symbol: $beta$")

# plotting error bars was never easier
library("dplyr", warn.conflicts = FALSE)
df2 <- df |> 
  as_tibble() |> 
  slice(1:25) |>
  filter(var_1 <= 50) |> 
  mutate(error1 = var_2 * 0.9,
         error2 = var_2 * 1.1)

df2

df2 |> 
  plot2(var_1, var_2, var_3, type = "col", datalabels = FALSE, alpha = 0.25, width = 0.75) |> 
  # adding error bars was never easier - just reference the lower and upper values
  add_errorbar(error1, error2)

# adding sf objects is just as convenient as all else
plot2(netherlands)
plot2(netherlands) |>
  add_sf(netherlands, colour_fill = NA, colour = "red", linewidth = 1)

---

Example Data Set with Admitted Patients

Description

An auto-generated data set containing fictitious patients admitted to hospitals.

Usage

admitted_patients

Format

A tibble/data.frame with 250 observations and 7 variables:

• date
  date of hospital admission

• patient_id
  ID of the patient (fictitious)

• gender
  gender of the patient

• age
  age of the patient

• age_group
  age group of the age of the patient, generated with AMR::age_groups()

• hospital
  ID of the hospital, from A to D

• ward
  type of ward, either ICU or Non-ICU

---

Create Interactive Plotly

Description

Transform a ggplot2/plot2 object to an interactive plot using the Plotly R Open Source Graphing Library.

Usage

as_plotly(plot, ...)

plotly_style(plot, ...)

Arguments

plot	a ggplot2 plot
...	In case of as_plotly(): arguments to pass on to layout() to change the Plotly layout object In case of plotly_style(): arguments to pass on to style() to change the Plotly style object

Examples

mtcars |>
  plot2(mpg, hp) |> 
  as_plotly()
  
mtcars |>
  plot2(mpg, hp) |> 
  as_plotly(dragmode = "pan") |>
  plotly_style(marker.line.color = "red",
               hoverinfo = "y")

---

Use Decimal Comma?

Description

These functions determine which characters the decimal mark and big mark should be that are used in plotting. They base the determination on getOption("OutDec"), which is also what base::format() uses.

Usage

dec_mark()

big_mark()

Details

If the option "dec_mark" is set, that value will be used for dec_mark() if it is either a comma or a full stop.

At default, big_mark() returns a full stop if dec_mark() returns a comma, and a space otherwise. If the option "big_mark" is set, that value will be used if it is either a comma (",") or a full stop (".") or a space (" ") or an empty character ("").

Examples

# at default, this follows `getOption("OutDec")`:
dec_mark()
# and big_mark() returns a space if dec_mark() returns ".":
big_mark()

# you you can set options to alter behaviour:
options(dec_mark = ",", big_mark = ".")
dec_mark()
big_mark()

options(dec_mark = ",", big_mark = NULL)
dec_mark()
big_mark()

options(big_mark = ",")
dec_mark()
big_mark()

# clean up
options(dec_mark = NULL, big_mark = NULL)

---

Colours from R, Viridis and More

Description

Colours from R, viridis and more. The output prints in the console with the actual colours.

Usage

get_colour(x, length = 1, opacity = 0)

register_colour(...)

## S3 method for class 'colour'
as.character(x, ...)

## S3 method for class 'colour'
print(x, ...)

add_white(x, white)

Arguments

x	colour or colour palette name. Input can be: One of the colourblind-safe viridisLite palettes: "viridis" "magma" "inferno" "plasma" "cividis" "rocket" "mako" "turbo" One of the built-in palettes in R (these are from R 4.4.1): "Accent" "Alphabet" "Classic Tableau" "Dark 2" "Okabe-Ito" "Paired" "Pastel 1" "Pastel 2" "Polychrome 36" "R3" "R4" "Set 1" "Set 2" "Set 3" "Tableau 10" "ggplot2" "grayscale" "greyscale" "heatmap" "rainbow" "terrain" "topo" One of the 657 built-in colours() in R (even case-insensitive), such as "brown3", "darkorchid1", "dodgerblue2", "lemonchiffon4", "snow2" One of the pre-registered colours using register_colour()
length	size of the vector to be returned
opacity	amount of opacity (0 = solid, 1 = transparent)
...	named vectors with known, valid colours. They must be coercible with get_colour().
white	number between ⁠[0, 1]⁠ to add white to x

Details

A palette from R will be expanded where needed, so even get_colour("R4", length = 20) will work, despite "R4" only supporting a maximum of eight colours.

Value

character vector in HTML format (i.e., "#AABBCC") with new class colour

Examples

get_colour(c("red", "tan1", "#ffa", "FFAA00"))

par(mar = c(0.5, 2.5, 1.5, 0)) # set plot margins for below plots

# all colourblind-safe colour palettes from the famous viridisLite package
barplot(1:7,
        col = get_colour("viridis", 7))
barplot(1:7,
        col = get_colour("magma", 7))

barplot(8:1,
        col = get_colour("R4", 8),
        main = "Some palettes have only 8 colours...")
barplot(20:1,
        col = get_colour("R4", 20),
        main = "Not anymore!")


# Registering Colours --------------------------------------------------

# to register colours, use named input - the values will be evaluated
# with get_colour()
get_colour("red123")
register_colour(red123 = "red", red456 = "#ff0000", red789 = "f00")
get_colour("red123")
get_colour("red456")
get_colour("red789")

# you can also register a group name
register_colour(red_group = c("red123", "ff4400", "red3", "red4"))
get_colour("red_group")
get_colour("red_group", 3)

# Registering colours is ideal for your (organisational) style in plots.
# Let's say these are your style:
register_colour(navy_blue = "#1F3A93",
                burnt_orange = "#D35400",
                forest_green = "#2C6F47",
                goldenrod_yellow = "#DAA520",
                slate_grey = "#708090",
                plum_purple = "#8E4585")

# Then register the whole colour list too:
register_colour(my_organisation = c("navy_blue", "burnt_orange",
                                    "forest_green", "goldenrod_yellow",
                                    "slate_grey", "plum_purple"))
# Check that it works:
get_colour("my_organisation", length = 6)

# Now use it in plots as you like:
iris |>
  plot2(x = Species, y = where(is.double), colour = "my_organisation")

# Or even set the option to use it in any future plot:
options(plot2.colour = "my_organisation")

iris |>
  plot2(x = Species, y = where(is.double))

# reset option again
options(plot2.colour = NULL)


# Use add_white() to add white to existing colours:
colours <- get_colour("R4", 6)
colours
add_white(colours, 0.25)
add_white(colours, 0.5)
add_white(colours, 0.75)

add_white("red", 1/128)
add_white("red", 1/64)
add_white("red", 1/32)

---

Get Plot Title

Description

Get the title of the plot, or a default value. If the title is not set in a plot, this function tries to generate one from the plot mapping.

Usage

get_plot_title(plot, valid_filename = TRUE, default = NULL)

Arguments

plot	a ggplot2 plot
valid_filename	a logical to indicate whether the returned value should be a valid filename, defaults to TRUE
default	the default value, if a plot title is absent

Examples

without_title <- plot2(mtcars)
with_title <- plot2(mtcars, title = "Plotting **mpg** vs. **cyl**!")

# default is a guess:
get_plot_title(without_title)
get_plot_title(without_title, valid_filename = FALSE)
get_plot_title(with_title)
get_plot_title(with_title, valid_filename = FALSE)

# unless 'default' is set (only affects plots without title):
get_plot_title(without_title, default = "title")
get_plot_title(with_title, default = "title")

---

Label Euro currencies

Description

Format numbers as currency, rounding values to dollars or cents using a convenient heuristic.

Usage

euros(x, big.mark = big_mark(), decimal.mark = dec_mark(), ...)

dollars(x, big.mark = big_mark(), decimal.mark = dec_mark(), ...)

Arguments

x	values
big.mark	thousands separator, defaults to big_mark()
decimal.mark	decimal mark, defaults to dec_mark()
...	any argument to give to the geom. This will override automatically-set settings for the geom.

Examples

## Not run: 
profit <- data.frame(group = LETTERS[1:4],
                     profit = runif(4, 10000, 25000))

profit |>
  plot2(y.labels = euros,
        datalabels = FALSE)
        
profit |>
  plot2(y.labels = euros,
        datalabels.format = euros)

## End(Not run)

---

Convert Markdown to Plotmath Expression

Description

This function converts common markdown language to an R plotmath expression. plot2() uses this function internally to convert plot titles and axis titles.

Usage

md_to_expression(x)

Arguments

x	text to convert, only the first value will be evaluated

Details

This function only supports common markdown (italic, bold, bold-italic, subscript, superscript), but also supports some additional functionalities for more advanced expressions using R plotmath. Please see Examples.

In plot2(), this function can be also set to argument category.labels to print the data values as expressions:

• plot2(..., category.labels = md_to_expression)

Value

An expression if x is length 1, or a list of expressions otherwise

Examples

# use '*' for italics, not '_', to prevent conflicts with variable naming
md_to_expression("this is *italic* text, this is _not italic_ text")

md_to_expression("this is **bold** text")

md_to_expression("this is ***bold and italic*** text")

# subscript and superscript can be done in HTML or markdown with curly brackets:
md_to_expression("this is some<sub>subscripted text</sub>, this is also_{subscripted} text")
md_to_expression("this is some<sup>superscripted text</sup>, this is also^{superscripted} text")

# use $...$ to use any plotmath expression as-is (see ?plotmath):
md_to_expression("text $omega$ text, $a[x]$")

mtcars |>
  plot2(mpg, hp,
        title = "*These are* the **Greek** lower $omega$ and upper $Omega$",
        x.title = "x_{mpg}",
        y.title = "y_{hp}")
        
mtcars |> 
  plot2(mpg, hp,
        title = "$f[X](x)==frac(1, sigma*sqrt(2*pi))*plain(e)^{frac(-(x-mu)^2, 2*sigma^2)}$",
        subtitle = "Some insane $widehat(plotmath)$ title")

---

Move a ggplot Layer

Description

Use this function to move a certain plot layer up or down. This function returns a ggplot object.

Usage

move_layer(plot, move = -1, layer = length(plot$layers))

Arguments

plot	a ggplot object
move	number of layers to move layer up or down
layer	the layer to affect, defaults to top layer

---

Example Geography Data Set: the Netherlands

Description

A data set containing the geometies of the twelve provinces of the Netherlands, according to Statistics Netherlands (2021).

Usage

netherlands

Format

A data.frame with 12 observations and 3 variables:

• province
  name of the Dutch province

• area_km2
  area in square kilometres

• geometry
  geometry of the province, of class sfc_MULTIPOLYGON/sfc

---

Conveniently Create a New ggplot

Description

The plot2() function is a convenient wrapper around many ggplot2 functions. By design, the ggplot2 package requires users to use a lot of functions and manual settings, while the plot2() function does all the heavy lifting automatically and only requires users to define some arguments in one single function, greatly increases convenience.

Moreover, plot2() allows for in-place calculation of y, all axes, and all axis labels, often preventing the need to use group_by(), count(), mutate(), or summarise().

See plot2-methods for all implemented methods for different object classes.

Usage

plot2(
  .data,
  x = NULL,
  y = NULL,
  category = NULL,
  facet = NULL,
  type = NULL,
  x.title = TRUE,
  y.title = TRUE,
  category.title = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  title.linelength = 60,
  title.colour = getOption("plot2.colour_font_primary", "black"),
  subtitle.linelength = 60,
  subtitle.colour = getOption("plot2.colour_font_secondary", "grey35"),
  na.replace = "",
  na.rm = FALSE,
  facet.position = "top",
  facet.fill = NULL,
  facet.bold = TRUE,
  facet.italic = FALSE,
  facet.size = 10,
  facet.margin = 8,
  facet.repeat_lbls_x = TRUE,
  facet.repeat_lbls_y = NULL,
  facet.fixed_y = NULL,
  facet.fixed_x = NULL,
  facet.drop = FALSE,
  facet.nrow = NULL,
  facet.relative = FALSE,
  x.date_breaks = NULL,
  x.date_labels = NULL,
  x.date_remove_years = NULL,
  category.focus = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  colour_fill = NULL,
  colour_opacity = 0,
  x.lbl_angle = 0,
  x.lbl_align = NULL,
  x.lbl_italic = FALSE,
  x.lbl_taxonomy = FALSE,
  x.remove = FALSE,
  x.position = "bottom",
  x.max_items = Inf,
  x.max_txt = "(rest, x%n)",
  category.max_items = Inf,
  category.max_txt = "(rest, x%n)",
  facet.max_items = Inf,
  facet.max_txt = "(rest, x%n)",
  x.breaks = NULL,
  x.n_breaks = NULL,
  x.transform = "identity",
  x.expand = NULL,
  x.limits = NULL,
  x.labels = NULL,
  x.character = NULL,
  x.drop = FALSE,
  x.mic = FALSE,
  x.zoom = FALSE,
  y.remove = FALSE,
  y.24h = FALSE,
  y.age = FALSE,
  y.scientific = NULL,
  y.percent = FALSE,
  y.percent_break = 0.1,
  y.breaks = NULL,
  y.n_breaks = NULL,
  y.limits = NULL,
  y.labels = NULL,
  y.expand = NULL,
  y.transform = "identity",
  y.position = "left",
  y.zoom = FALSE,
  y_secondary = NULL,
  y_secondary.type = type,
  y_secondary.title = TRUE,
  y_secondary.colour = colour,
  y_secondary.colour_fill = colour_fill,
  y_secondary.scientific = NULL,
  y_secondary.percent = FALSE,
  y_secondary.labels = NULL,
  category.labels = NULL,
  category.percent = FALSE,
  category.breaks = NULL,
  category.limits = NULL,
  category.expand = 0,
  category.midpoint = NULL,
  category.transform = "identity",
  category.date_breaks = NULL,
  category.date_labels = NULL,
  category.character = NULL,
  x.sort = NULL,
  category.sort = TRUE,
  facet.sort = TRUE,
  x.complete = NULL,
  category.complete = NULL,
  facet.complete = NULL,
  datalabels = TRUE,
  datalabels.round = ifelse(y.percent, 2, 1),
  datalabels.format = "%n",
  datalabels.colour = "grey25",
  datalabels.colour_fill = NULL,
  datalabels.size = (3 * text_factor),
  datalabels.angle = 0,
  datalabels.lineheight = 1,
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  summarise_function = base::sum,
  stacked = FALSE,
  stackedpercent = FALSE,
  horizontal = FALSE,
  reverse = horizontal,
  smooth = NULL,
  smooth.method = NULL,
  smooth.formula = NULL,
  smooth.se = TRUE,
  smooth.level = 0.95,
  smooth.alpha = 0.25,
  smooth.linewidth = 0.75,
  smooth.linetype = 3,
  smooth.colour = NULL,
  size = NULL,
  linetype = 1,
  linewidth = NULL,
  binwidth = NULL,
  width = NULL,
  jitter_seed = NA,
  violin_scale = "count",
  legend.position = NULL,
  legend.title = NULL,
  legend.reverse = FALSE,
  legend.barheight = 6,
  legend.barwidth = 1.5,
  legend.nbin = 300,
  legend.italic = FALSE,
  sankey.node_width = 0.15,
  sankey.node_whitespace = 0.03,
  sankey.alpha = 0.5,
  sankey.remove_axes = NULL,
  zoom = FALSE,
  sep = " / ",
  print = FALSE,
  text_factor = 1,
  font = getOption("plot2.font"),
  theme = getOption("plot2.theme", "theme_minimal2"),
  background = getOption("plot2.colour_background", "white"),
  markdown = TRUE,
  data = NULL,
  ...
)

Arguments

.data	data to plot
x	plotting 'direction' for the x axis. This can be: A single variable from .data, such as x = column1 A function to calculate over one or more variables from .data, such as x = format(column1, "%Y"), or x = ifelse(column1 == "A", "Group A", "Other") Multiple variables from .data, such as x = c(column1, column2, column2), or using selection helpers such as x = where(is.character) or x = starts_with("var_") (only allowed and required for Sankey plots using type = "sankey")
y	values to use for plotting along the y axis. This can be: A single variable from .data, such as y = column1 Multiple variables from .data, such as y = c(column1, column2) or y = c(name1 = column1, "name 2" = column2), or using selection helpers such as y = where(is.double) or y = starts_with("var_") (multiple variables only allowed if category is not set) A function to calculate over .data returning a single value, such as y = n() for the row count, or based on other variables such as y = n_distinct(person_id), y = max(column1), or y = median(column2) / column3 A function to calculate over .data returning multiple values, such as y = quantile(column1, c(0.25, 0.75)) or y = range(age) (multiple values only allowed if category is not set)
category, facet	plotting 'direction' (category is called 'fill' and 'colour' in ggplot2). This can be: A single variable from .data, such as category = column1 A function to calculate over one or more variables from .data, such as category = median(column2) / column3, or facet = ifelse(column1 == "A", "Group A", "Other") Multiple variables from .data, such as facet = c(column1, column2) (use sep to control the separator character) One or more variables from .data using selection helpers, such as category = where(is.double) or facet = starts_with("var_") The category can also be a date or date/time (class Date or POSIXt).
type, y_secondary.type	type of visualisation to use. This can be: A ggplot2 geom name or their abbreviation such as "col" and "point". All geoms are supported (including geom_blank()). Full function names can be used (e.g., "geom_histogram"), but they can also be abbreviated (e.g., "h", "hist"). The following geoms can be abbreviated by their first character: area ("a"), boxplot ("b"), column ("c"), histogram ("h"), jitter ("j"), line ("l"), point ("p"), ribbon ("r"), and violin ("v"). Please note: in ggplot2, 'bars' and 'columns' are equal, while it is common to many people that 'bars' are oriented horizontally and 'columns' are oriented vertically since Microsoft Excel has been using these terms this way for many years. For this reason, type = "bar" will set type = "col" and horizontal = TRUE. One of these additional types: "barpercent" (short: "bp"), which is effectively a shortcut to set type = "col" and horizontal = TRUE and x.max_items = 10 and x.sort = "freq-desc" and datalabels.format = "%n (%p)". "linedot" (short: "ld"), which sets type = "line" and adds two point geoms using add_point(); one with large white dots and one with smaller dots using the colours set in colour. This is essentially equal to base R plot(..., type = "b") but with closed shapes. "dumbbell" (short: "d"), which sets type = "point" and horizontal = TRUE, and adds a line between the points (using geom_segment()). The line colour cannot be changed. This plot type is only possible when the category has two distinct values. "sankey" (short: "s") creates a Sankey plots using category for the flows and requires x to contain multiple variables from .data. At default, it also sets x.expand = c(0.05, 0.05) and y.limits = c(NA, NA) and y.expand = c(0.01, 0.01). The so-called 'nodes' (the 'blocks' with text) are considered the datalabels, so you can set the text size and colour of the nodes using datalabels.size, datalabels.colour, and datalabels.colour_fill. The transparency of the flows can be set using sankey.alpha, and the width of the nodes can be set using sankey.node_width. Sankey plots can also be flipped using horizontal = TRUE. Left blank. In this case, the type will be determined automatically: "boxplot" if there is no x axis or if the length of unique values per x axis item is at least 3, "point" if both the y and x axes are numeric, and the option "plot2.default_type" otherwise (which defaults to "col"). Use type = "blank" or type = "geom_blank" to not add a geom.
title, subtitle, caption, tag, x.title, y.title, category.title, legend.title, y_secondary.title	a title to use. This can be: A character, which supports markdown by using md_to_expression() internally if markdown = TRUE (which is the default) A function to calculate over .data, such as title = paste("Based on n =", n_distinct(person_id), "individuals") or subtitle = paste("Total rows:", n()), see Examples An expression, e.g. using parse(text = "...") The category.title defaults to TRUE if the legend items are numeric.
title.linelength	maximum number of characters per line in the title, before a linebreak occurs
title.colour	text colour of the title
subtitle.linelength	maximum number of characters per line in the subtitle, before a linebreak occurs
subtitle.colour	text colour of the subtitle
na.replace	character to put in place of NA values if na.rm = FALSE
na.rm	remove NA values from showing in the plot
facet.position, facet.fill, facet.bold, facet.italic, facet.size, facet.margin, facet.repeat_lbls_x, facet.repeat_lbls_y, facet.drop, facet.nrow, facet.relative	additional settings for the plotting direction facet
facet.fixed_y	a logical to indicate whether all y scales should have the same limits. Defaults to TRUE only if the coefficient of variation (standard deviation divided by mean) of the maximum values of y is less than 25%.
facet.fixed_x	a logical to indicate whether all x scales should have the same breaks. This acts like the inverse of x.drop.
x.date_breaks	breaks to use when the x axis contains dates, will be determined automatically if left blank. This accepts values such as "1 day" and "2 years".
x.date_labels	labels to use when the x axis contains dates, will be determined automatically if left blank. This accepts 'Excel' date-language such as "d mmmm yyyy".
x.date_remove_years	a logical to indicate whether the years of all x values must be unified. This will set the years of all x values to 1970 if the data does not contain a leap year, and to 1972 otherwise. This allows to plot years on the category while maintaining a date range on x. The default is FALSE, unless category contains all years present in x.
category.focus	a value of category that should be highlighted, meaning that all other values in category will be greyed out. This can also be a numeric value between 1 and the length of unique values of category, e.g. category.focus = 2 to focus on the second legend item.
colour	get_colour(s) to set, will be evaluated with get_colour() if set. This can also be one of the viridis colours with automatic implementation for any plot: "viridis", "magma", "inferno", "plasma", "cividis", "rocket", "mako" or "turbo". Also, this can also be a named vector to match values of category, see Examples. Using a named vector can also be used to manually sort the values of category.
colour_fill	get_colour(s) to be used for filling, will be determined automatically if left blank and will be evaluated with get_colour()
colour_opacity	amount of opacity for colour/colour_fill (0 = solid, 1 = transparent)
x.lbl_angle	angle to use for the x axis in a counter-clockwise direction (i.e., a value of 90 will orient the axis labels from bottom to top, a value of 270 will orient the axis labels from top to bottom)
x.lbl_align	alignment for the x axis between 0 (left aligned) and 1 (right aligned)
x.lbl_italic	logical to indicate whether the x labels should in in italics
x.lbl_taxonomy	a logical to transform all words of the x labels into italics that are in the microorganisms data set of the AMR package. This uses md_to_expression() internally and will set x.labels to parse expressions.
x.remove, y.remove	a logical to indicate whether the axis labels and title should be removed
x.position, y.position	position of the axis
x.max_items, category.max_items, facet.max_items	number of maximum items to use, defaults to infinite. All other values will be grouped and summarised using the summarise_function function. Please note: the sorting will be applied first, allowing to e.g. plot the top n most frequent values of the x axis by combining x.sort = "freq-desc" with ⁠x.max_items =⁠ n.
x.max_txt, category.max_txt, facet.max_txt	the text to use of values not included number of ⁠*.max_items⁠. The placeholder ⁠%n⁠ will be replaced with the outcome of the summarise_function function, the placeholder ⁠%p⁠ will be replaced with the percentage.
x.breaks, y.breaks	a breaks function or numeric vector to use for the axis
x.n_breaks, y.n_breaks	number of breaks, only useful if x.breaks cq. y.breaks is NULL
x.transform, y.transform, category.transform	a transformation function to use, e.g. "log2". This can be: "asinh", "asn", "atanh", "boxcox", "compose", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt", "time", "timespan", "yj".
x.expand, y.expand	expansion to use for the axis, can be length 1 or 2. x.expand defaults to 0.5 and y.expand defaults to 0.25, except for sf objects (then both default to 0).
x.limits, y.limits	limits to use for the axis, can be length 1 or 2. Use NA for the highest or lowest value in the data, e.g. y.limits = c(0, NA) to have the y scale start at zero.
x.labels, y.labels, y_secondary.labels	a labels function or character vector to use for the axis
x.character	a logical to indicate whether the values of the x axis should be forced to character. The default is FALSE, except for years (values between 2000 and 2050) and months (values from 1 to 12).
x.drop	logical to indicate whether factor levels should be dropped
x.mic	logical to indicate whether the x axis should be formatted as MIC values, by dropping all factor levels and adding missing factors of 2
x.zoom, y.zoom	a logical to indicate if the axis should be zoomed on the data, by setting x.limits = c(NA, NA) and x.expand = 0 for the x axis, or y.limits = c(NA, NA) and y.expand = 0 for the y axis
y.24h	a logical to indicate whether the y labels and breaks should be formatted as 24-hour sequences
y.age	a logical to indicate whether the y labels and breaks should be formatted as ages in years
y.scientific, y_secondary.scientific	a logical to indicate whether the y labels should be formatted in scientific notation. Defaults to TRUE only if the range of the y values spans more than 10e5.
y.percent, y_secondary.percent	a logical to indicate whether the y labels should be formatted as percentages
y.percent_break	a value on which the y axis should have breaks
y_secondary	values to use for plotting along the secondary y axis. This functionality is poorly supported by ggplot2 and might give unexpected results. Setting the secondary y axis will set the colour to the axis titles.
y_secondary.colour, y_secondary.colour_fill	colours to set for the secondary y axis, will be evaluated with get_colour()
category.labels, category.percent, category.breaks, category.expand, category.midpoint	settings for the plotting direction category.
category.limits	limits to use for a numeric category, can be length 1 or 2. Use NA for the highest or lowest value in the data, e.g. category.limits = c(0, NA) to have the scale start at zero.
category.date_breaks	breaks to use when the category contains dates, will be determined automatically if left blank. This will be passed on to seq.Date(by = ...) and thus can be: a number, taken to be in days, or a character string containing one of "day", "week", "month", "quarter" or "year" (optionally preceded by an integer and a space, and/or followed by "s").
category.date_labels	labels to use when the category contains dates, will be determined automatically if left blank. This accepts 'Excel' date-language such as "d mmmm yyyy".
category.character	a logical to indicate whether the values of the category should be forced to character. The default is FALSE, except for years (values between 2000 and 2050) and months (values from 1 to 12).
x.sort, category.sort, facet.sort	sorting of the plotting direction, defaults to TRUE, except for continuous values on the x axis (such as dates and numbers). Applying one of the sorting methods will transform the values to an ordered factor, which ggplot2 uses to orient the data. Valid values are: A manual vector of values TRUE: sort factors on their levels, otherwise sort ascending on alphabet, while maintaining numbers in the text (numeric sort) FALSE: sort according to the order in the data NULL: do not sort/transform at all "asc" or "alpha": sort as TRUE "desc": sort factors on their reversed levels, otherwise sort descending on alphabet, while maintaining numbers in the text (numeric sort) "order" or "inorder": sort as FALSE "freq" or "freq-desc": sort descending according to the frequencies of y computed by summarise_function (highest value first) "freq-asc": sort ascending according to the frequencies of y computed by summarise_function (lowest value first)
x.complete, category.complete, facet.complete	a value to complete the data. This makes use of tidyr::full_seq() and tidyr::complete(). For example, using x.complete = 0 will apply data |> complete(full_seq(x, ...), fill = list(x = 0)). Using value TRUE (e.g., x.complete = TRUE) is identical to using value 0.
datalabels	values to show as datalabels, see also datalabels.format. This can be: Left blank. This will default to the values of y in column-type plots, or when plotting spatial 'sf' data, the values of the first column. It will print a maximum of 25 labels unless datalabels = TRUE. TRUE or FALSE to force or remove datalabels A function to calculate over .data, such as datalabels = paste(round(column1), "\n", column2)
datalabels.round	number of digits to round the datalabels, applies to both "%n" and "%p" for replacement (see datalabels.format)
datalabels.format	format to use for datalabels. This can be a function (such as euros()) or a text. For the text, "%n" will be replaced by the count number, and "%p" will be replaced by the percentage of the total count. Use datalabels.format = NULL to not transform the datalabels.
datalabels.colour, datalabels.colour_fill, datalabels.size, datalabels.angle, datalabels.lineheight	settings for the datalabels
decimal.mark	decimal mark, defaults to dec_mark()
big.mark	thousands separator, defaults to big_mark()
summarise_function	a function to use if the data has to be summarised, see Examples. This can also be NULL, which will be converted to function(x) x.
stacked	a logical to indicate that values must be stacked
stackedpercent	a logical to indicate that values must be 100% stacked
horizontal	a logical to turn the plot 90 degrees using coord_flip(). This option also updates some theme options, so that e.g., x.lbl_italic will still apply to the original x axis.
reverse	a logical to reverse the values of category. Use legend.reverse to reverse the legend of category.
smooth	a logical to add a smooth. In histograms, this will add the density count as an overlaying line (default: TRUE). In all other cases, a smooth will be added using geom_smooth() (default: FALSE).
smooth.method, smooth.formula, smooth.se, smooth.level, smooth.alpha, smooth.linewidth, smooth.linetype, smooth.colour	settings for smooth
size	size of the geom. Defaults to 2 for geoms point and jitter, 5 for a dumbbell plots (using type = "dumbbell"), and to 0.75 otherwise.
linetype	linetype of the geom, only suitable for geoms that draw lines. Defaults to 1.
linewidth	linewidth of the geom, only suitable for geoms that draw lines. Defaults to: 0.5 for geoms that have no area (such as line), and for geoms boxplot/violin 0.1 for sf 0.25 for geoms that are continous and have fills (such as area) 1.0 for dumbbell plots (using type = "dumbbell") 0.5 otherwise (such as histogram and area)
binwidth	width of bins (only useful for geom = "histogram"), can be specified as a numeric value or as a function that calculates width from x, see geom_histogram(). It defaults to approx. diff(range(x)) divided by 12 to 22 based on the data.
width	width of the geom. Defaults to 0.75 for geoms boxplot, violin and jitter, and to 0.5 otherwise.
jitter_seed	seed (randomisation factor) to be set when using type = "jitter"
violin_scale	scale to be set when using type = "violin", can also be set to "area"
legend.position	position of the legend, must be "top", "right", "bottom", "left" or "none" (or NA or NULL), can be abbreviated. Defaults to "right" for numeric category values and 'sf' plots, and "top" otherwise.
legend.reverse, legend.barheight, legend.barwidth, legend.nbin, legend.italic	other settings for the legend
sankey.node_width	width of the vertical nodes in a Sankey plot (i.e., when type = "sankey")
sankey.node_whitespace	whitespace between the nodes
sankey.alpha	alpha of the flows in a Sankey plot (i.e., when type = "sankey")
sankey.remove_axes	logical to indicate whether all axes must be removed in a Sankey plot (i.e., when type = "sankey")
zoom	a logical to indicate if the plot should be scaled to the data, i.e., not having the x and y axes to start at 0. This will set x.zoom = TRUE and y.zoom = TRUE.
sep	separator character to use if multiple columns are given to either of the three directions: x, category and facet, e.g. facet = c(column1, column2)
print	a logical to indicate if the result should be printed instead of just returned
text_factor	text factor to use, which will apply to all texts shown in the plot
font	font (family) to use, can be set with options(plot2.font = "..."). Can be any installed system font or any of the > 1400 font names from Google Fonts. When using custom fonts in R Markdown, be sure to set the chunk option fig.showtext = TRUE, otherwise an informative error will be generated.
theme	a valid ggplot2 theme to apply, or NULL to use the default theme_grey(). This argument accepts themes (e.g., theme_bw()), functions (e.g., theme_bw) and characters themes (e.g., "theme_bw"). The default is theme_minimal2(), but can be set with options(plot2.theme = "...").
background	the background colour of the entire plot, can also be NA to remove it. Will be evaluated with get_colour(). Only applies when theme is not NULL.
markdown	a logical to turn all labels and titles into plotmath expressions, by converting common markdown language using the md_to_expression() function (defaults to TRUE)
data	substitute for .data, used in formula notation, e.g., plot2(hp ~ mpg, data = mtcars)
...	any argument to give to the geom. This will override automatically-set settings for the geom.

Details

The plot2() function is a convenient wrapper around many ggplot2 functions such as ggplot(), aes(), geom_col(), facet_wrap(), labs(), etc., and provides:

• Writing as few lines of codes as possible

• Easy plotting in three 'directions': x (the regular x axis), category (replaces 'fill' and 'colour') and facet

• Automatic setting of these 'directions' based on the input data

• Setting in-place calculations for all plotting directions and even y

• Easy way for sorting data in many ways (such as on alphabet, numeric value, frequency, original data order), by setting a single argument for the 'direction': x.sort, category.sort and facet.sort

• Easy limiting values, e.g. by setting x.max_items = 5 or category.max_items = 5

• Markdown support for any title text, with any theme

• Integrated support for any Google Font and any installed system font

• An extra clean, minimalistic theme with a lot of whitespace (but without unnecessary margins) that is ideal for printing: theme_minimal2()

• Some conveniences from Microsoft Excel:

  • The y axis starts at 0 if possible

  • The y scale expands at the top to be better able to interpret all data points

  • Date breaks can be written in a human-readable format (such as "d mmm yyyy")

  • Labels with data values can easily be printed and are automatically determined

• Support for any ggplot2 extension based on ggplot2::fortify()

The ggplot2 package in conjunction with the tidyr, forcats and cleaner packages can provide above functionalities, but the goal of the plot2() function is to generalise this into one function. The generic plot2() function currently has 150 arguments, all with a default value. Less typing, faster coding.

Value

a ggplot object

Examples

options(plot2.colour = NULL, plot2.colour_sf_fill = NULL)

head(iris)

# no variables determined, so plot2() will try for itself -
# the type will be points since the first two variables are numeric
iris |>
  plot2()

# if x and y are set, no additional mapping will be set:
iris |> 
  plot2(Sepal.Width, Sepal.Length)
iris |> 
  plot2(Species, Sepal.Length)

# the arguments are in this order: x, y, category, facet
iris |> 
  plot2(Sepal.Length, Sepal.Width, Petal.Length, Species)

iris |> 
  plot2(Sepal.Length, Sepal.Width, Petal.Length, Species,
        colour = "viridis") # set the viridis colours
      
iris |> 
  plot2(Sepal.Length, Sepal.Width, Petal.Length, Species,
        colour = c("white", "red", "black")) # set own colours

# y can also be multiple (named) columns
iris |> 
  plot2(x = Sepal.Length,
        y = c(Length = Petal.Length, Width = Petal.Width),
        category.title = "Petal property")
iris |>
  # with included selection helpers such as where(), starts_with(), etc.:
  plot2(x = Species, y = where(is.double))
  
# support for secondary y axis
mtcars |>
  plot2(x = mpg,
        y = hp,
        y_secondary = disp ^ 2, 
        y_secondary.scientific = TRUE,
        title = "Secondary y axis sets colour to the axis titles")


admitted_patients

# the arguments are in this order: x, y, category, facet
admitted_patients |>
  plot2(hospital, age)

admitted_patients |>
  plot2(hospital, age, gender)
  
admitted_patients |>
  plot2(hospital, age, gender, ward)
  
# or use any function for y
admitted_patients |>
  plot2(hospital, median(age), gender, ward)
admitted_patients |>
  plot2(hospital, n(), gender, ward)

admitted_patients |>
  plot2(x = hospital,
        y = age,
        category = gender,
        colour = c("F" = "#3F681C", "M" = "#375E97"),
        colour_fill = "#FFBB00AA",
        linewidth = 1.25,
        y.age = TRUE)

admitted_patients |>
  plot2(age, type = "hist")

# even titles support calculations, including support for {glue}
admitted_patients |>
  plot2(age, type = "hist",
        title = paste("Based on n =", n_distinct(patient_id), "patients"),
        subtitle = paste("Total rows:", n()),
        caption = glue::glue("From {n_distinct(hospital)} hospitals"),
        x.title = paste("Age ranging from", paste(range(age), collapse = " to ")))
 
# the default type is column, datalabels are automatically
# set in non-continuous types:
admitted_patients |> 
  plot2(hospital, n(), gender)
  
admitted_patients |> 
  plot2(hospital, n(), gender,
        stacked = TRUE)
        
admitted_patients |> 
  plot2(hospital, n(), gender,
        stackedpercent = TRUE)

# two categories might benefit from a dumbbell plot:
admitted_patients |> 
  plot2(hospital, median(age), gender, type = "dumbbell")
 
# sort on any direction:
admitted_patients |> 
  plot2(hospital, n(), gender,
        x.sort = "freq-asc",
        stacked = TRUE)

admitted_patients |> 
  plot2(hospital, n(), gender,
        x.sort = c("B", "D", "A"), # missing values ("C") will be added
        category.sort = "alpha-desc",
        stacked = TRUE)
        
# support for Sankey plots
Titanic |> # a table from base R
  plot2(x = c(Age, Class, Survived),
        category = Sex,
        type = "sankey")

# matrix support, such as for cor()
correlation_matrix <- cor(mtcars)
class(correlation_matrix)
head(correlation_matrix)
correlation_matrix |> 
  plot2()

correlation_matrix |> 
  plot2(colour = c("blue3", "white", "red3"),
        datalabels = TRUE,
        category.title = "*r*-value",
        title =  "Correlation matrix")


# plot2() supports all S3 extensions available through
# ggplot2::fortify(), such as regression models:
lm(mpg ~ hp, data = mtcars) |> 
  plot2(x = mpg ^ -3,
        y = hp ^ 2,
        smooth = TRUE,
        smooth.method = "lm",
        smooth.formula = "y ~ log(x)",
        title = "Titles/captions *support* **markdown**",
        subtitle = "Axis titles contain the square notation: x^2")

# sf objects (geographic plots, 'simple features') are also supported
if (require("sf")) {
  netherlands |> 
    plot2(datalabels = paste0(province, "\n", round(area_km2)))
}

# support for any system or Google font
mtcars |>
  plot2(mpg, hp, font = "Rock Salt",
        title = "This plot uses a Google Font")

---

Methods for plot2()

Description

These are the implemented methods for different S3 classes to be used in plot2(). Since they have an extensive list of arguments, they are placed here on a separate manual page.

Usage

## Default S3 method:
plot2(
  .data,
  x = NULL,
  y = NULL,
  category = NULL,
  facet = NULL,
  type = NULL,
  x.title = TRUE,
  y.title = TRUE,
  category.title = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  title.linelength = 60,
  title.colour = getOption("plot2.colour_font_primary", "black"),
  subtitle.linelength = 60,
  subtitle.colour = getOption("plot2.colour_font_secondary", "grey35"),
  na.replace = "",
  na.rm = FALSE,
  facet.position = "top",
  facet.fill = NULL,
  facet.bold = TRUE,
  facet.italic = FALSE,
  facet.size = 10,
  facet.margin = 8,
  facet.repeat_lbls_x = TRUE,
  facet.repeat_lbls_y = NULL,
  facet.fixed_y = NULL,
  facet.fixed_x = NULL,
  facet.drop = FALSE,
  facet.nrow = NULL,
  facet.relative = FALSE,
  x.date_breaks = NULL,
  x.date_labels = NULL,
  x.date_remove_years = NULL,
  category.focus = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  colour_fill = NULL,
  colour_opacity = 0,
  x.lbl_angle = 0,
  x.lbl_align = NULL,
  x.lbl_italic = FALSE,
  x.lbl_taxonomy = FALSE,
  x.remove = FALSE,
  x.position = "bottom",
  x.max_items = Inf,
  x.max_txt = "(rest, x%n)",
  category.max_items = Inf,
  category.max_txt = "(rest, x%n)",
  facet.max_items = Inf,
  facet.max_txt = "(rest, x%n)",
  x.breaks = NULL,
  x.n_breaks = NULL,
  x.transform = "identity",
  x.expand = NULL,
  x.limits = NULL,
  x.labels = NULL,
  x.character = NULL,
  x.drop = FALSE,
  x.mic = FALSE,
  x.zoom = FALSE,
  y.remove = FALSE,
  y.24h = FALSE,
  y.age = FALSE,
  y.scientific = NULL,
  y.percent = FALSE,
  y.percent_break = 0.1,
  y.breaks = NULL,
  y.n_breaks = NULL,
  y.limits = NULL,
  y.labels = NULL,
  y.expand = NULL,
  y.transform = "identity",
  y.position = "left",
  y.zoom = FALSE,
  y_secondary = NULL,
  y_secondary.type = type,
  y_secondary.title = TRUE,
  y_secondary.colour = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.colour_fill = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.scientific = NULL,
  y_secondary.percent = FALSE,
  y_secondary.labels = NULL,
  category.labels = NULL,
  category.percent = FALSE,
  category.breaks = NULL,
  category.limits = NULL,
  category.expand = 0,
  category.midpoint = NULL,
  category.transform = "identity",
  category.date_breaks = NULL,
  category.date_labels = NULL,
  category.character = NULL,
  x.sort = NULL,
  category.sort = TRUE,
  facet.sort = TRUE,
  x.complete = NULL,
  category.complete = NULL,
  facet.complete = NULL,
  datalabels = TRUE,
  datalabels.round = ifelse(y.percent, 2, 1),
  datalabels.format = "%n",
  datalabels.colour = "grey25",
  datalabels.colour_fill = NULL,
  datalabels.size = (3 * text_factor),
  datalabels.angle = 0,
  datalabels.lineheight = 1,
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  summarise_function = base::sum,
  stacked = FALSE,
  stackedpercent = FALSE,
  horizontal = FALSE,
  reverse = horizontal,
  smooth = NULL,
  smooth.method = NULL,
  smooth.formula = NULL,
  smooth.se = TRUE,
  smooth.level = 0.95,
  smooth.alpha = 0.25,
  smooth.linewidth = 0.75,
  smooth.linetype = 3,
  smooth.colour = NULL,
  size = NULL,
  linetype = 1,
  linewidth = NULL,
  binwidth = NULL,
  width = NULL,
  jitter_seed = NA,
  violin_scale = "count",
  legend.position = NULL,
  legend.title = NULL,
  legend.reverse = FALSE,
  legend.barheight = 6,
  legend.barwidth = 1.5,
  legend.nbin = 300,
  legend.italic = FALSE,
  sankey.node_width = 0.15,
  sankey.node_whitespace = 0.03,
  sankey.alpha = 0.5,
  sankey.remove_axes = NULL,
  zoom = FALSE,
  sep = " / ",
  print = FALSE,
  text_factor = 1,
  font = getOption("plot2.font"),
  theme = getOption("plot2.theme", "theme_minimal2"),
  background = getOption("plot2.colour_background", "white"),
  markdown = TRUE,
  ...
)

## S3 method for class 'formula'
plot2(
  .data = NULL,
  x = NULL,
  y = NULL,
  category = NULL,
  facet = NULL,
  type = NULL,
  x.title = TRUE,
  y.title = TRUE,
  category.title = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  title.linelength = 60,
  title.colour = getOption("plot2.colour_font_primary", "black"),
  subtitle.linelength = 60,
  subtitle.colour = getOption("plot2.colour_font_secondary", "grey35"),
  na.replace = "",
  na.rm = FALSE,
  facet.position = "top",
  facet.fill = NULL,
  facet.bold = TRUE,
  facet.italic = FALSE,
  facet.size = 10,
  facet.margin = 8,
  facet.repeat_lbls_x = TRUE,
  facet.repeat_lbls_y = NULL,
  facet.fixed_y = NULL,
  facet.fixed_x = NULL,
  facet.drop = FALSE,
  facet.nrow = NULL,
  facet.relative = FALSE,
  x.date_breaks = NULL,
  x.date_labels = NULL,
  x.date_remove_years = NULL,
  category.focus = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  colour_fill = NULL,
  colour_opacity = 0,
  x.lbl_angle = 0,
  x.lbl_align = NULL,
  x.lbl_italic = FALSE,
  x.lbl_taxonomy = FALSE,
  x.remove = FALSE,
  x.position = "bottom",
  x.max_items = Inf,
  x.max_txt = "(rest, x%n)",
  category.max_items = Inf,
  category.max_txt = "(rest, x%n)",
  facet.max_items = Inf,
  facet.max_txt = "(rest, x%n)",
  x.breaks = NULL,
  x.n_breaks = NULL,
  x.transform = "identity",
  x.expand = NULL,
  x.limits = NULL,
  x.labels = NULL,
  x.character = NULL,
  x.drop = FALSE,
  x.mic = FALSE,
  x.zoom = FALSE,
  y.remove = FALSE,
  y.24h = FALSE,
  y.age = FALSE,
  y.scientific = NULL,
  y.percent = FALSE,
  y.percent_break = 0.1,
  y.breaks = NULL,
  y.n_breaks = NULL,
  y.limits = NULL,
  y.labels = NULL,
  y.expand = NULL,
  y.transform = "identity",
  y.position = "left",
  y.zoom = FALSE,
  y_secondary = NULL,
  y_secondary.type = type,
  y_secondary.title = TRUE,
  y_secondary.colour = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.colour_fill = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.scientific = NULL,
  y_secondary.percent = FALSE,
  y_secondary.labels = NULL,
  category.labels = NULL,
  category.percent = FALSE,
  category.breaks = NULL,
  category.limits = NULL,
  category.expand = 0,
  category.midpoint = NULL,
  category.transform = "identity",
  category.date_breaks = NULL,
  category.date_labels = NULL,
  category.character = NULL,
  x.sort = NULL,
  category.sort = TRUE,
  facet.sort = TRUE,
  x.complete = NULL,
  category.complete = NULL,
  facet.complete = NULL,
  datalabels = TRUE,
  datalabels.round = ifelse(y.percent, 2, 1),
  datalabels.format = "%n",
  datalabels.colour = "grey25",
  datalabels.colour_fill = NULL,
  datalabels.size = (3 * text_factor),
  datalabels.angle = 0,
  datalabels.lineheight = 1,
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  summarise_function = base::sum,
  stacked = FALSE,
  stackedpercent = FALSE,
  horizontal = FALSE,
  reverse = horizontal,
  smooth = NULL,
  smooth.method = NULL,
  smooth.formula = NULL,
  smooth.se = TRUE,
  smooth.level = 0.95,
  smooth.alpha = 0.25,
  smooth.linewidth = 0.75,
  smooth.linetype = 3,
  smooth.colour = NULL,
  size = NULL,
  linetype = 1,
  linewidth = NULL,
  binwidth = NULL,
  width = NULL,
  jitter_seed = NA,
  violin_scale = "count",
  legend.position = NULL,
  legend.title = NULL,
  legend.reverse = FALSE,
  legend.barheight = 6,
  legend.barwidth = 1.5,
  legend.nbin = 300,
  legend.italic = FALSE,
  sankey.node_width = 0.15,
  sankey.node_whitespace = 0.03,
  sankey.alpha = 0.5,
  sankey.remove_axes = NULL,
  zoom = FALSE,
  sep = " / ",
  print = FALSE,
  text_factor = 1,
  font = getOption("plot2.font"),
  theme = getOption("plot2.theme", "theme_minimal2"),
  background = getOption("plot2.colour_background", "white"),
  markdown = TRUE,
  data = NULL,
  ...
)

## S3 method for class 'freq'
plot2(
  .data,
  x = .data$item,
  y = .data$count,
  category = NULL,
  facet = NULL,
  type = NULL,
  x.title = "Item",
  y.title = "Count",
  category.title = TRUE,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  title.linelength = 60,
  title.colour = getOption("plot2.colour_font_primary", "black"),
  subtitle.linelength = 60,
  subtitle.colour = getOption("plot2.colour_font_secondary", "grey35"),
  na.replace = "",
  na.rm = FALSE,
  facet.position = "top",
  facet.fill = NULL,
  facet.bold = TRUE,
  facet.italic = FALSE,
  facet.size = 10,
  facet.margin = 8,
  facet.repeat_lbls_x = TRUE,
  facet.repeat_lbls_y = NULL,
  facet.fixed_y = NULL,
  facet.fixed_x = NULL,
  facet.drop = FALSE,
  facet.nrow = NULL,
  facet.relative = FALSE,
  x.date_breaks = NULL,
  x.date_labels = NULL,
  x.date_remove_years = NULL,
  category.focus = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  colour_fill = NULL,
  colour_opacity = 0,
  x.lbl_angle = 0,
  x.lbl_align = NULL,
  x.lbl_italic = FALSE,
  x.lbl_taxonomy = FALSE,
  x.remove = FALSE,
  x.position = "bottom",
  x.max_items = Inf,
  x.max_txt = "(rest, x%n)",
  category.max_items = Inf,
  category.max_txt = "(rest, x%n)",
  facet.max_items = Inf,
  facet.max_txt = "(rest, x%n)",
  x.breaks = NULL,
  x.n_breaks = NULL,
  x.transform = "identity",
  x.expand = NULL,
  x.limits = NULL,
  x.labels = NULL,
  x.character = NULL,
  x.drop = FALSE,
  x.mic = FALSE,
  x.zoom = FALSE,
  y.remove = FALSE,
  y.24h = FALSE,
  y.age = FALSE,
  y.scientific = NULL,
  y.percent = FALSE,
  y.percent_break = 0.1,
  y.breaks = NULL,
  y.n_breaks = NULL,
  y.limits = NULL,
  y.labels = NULL,
  y.expand = NULL,
  y.transform = "identity",
  y.position = "left",
  y.zoom = FALSE,
  y_secondary = NULL,
  y_secondary.type = type,
  y_secondary.title = TRUE,
  y_secondary.colour = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.colour_fill = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.scientific = NULL,
  y_secondary.percent = FALSE,
  y_secondary.labels = NULL,
  category.labels = NULL,
  category.percent = FALSE,
  category.breaks = NULL,
  category.limits = NULL,
  category.expand = 0,
  category.midpoint = NULL,
  category.transform = "identity",
  category.date_breaks = NULL,
  category.date_labels = NULL,
  category.character = NULL,
  x.sort = "freq-desc",
  category.sort = TRUE,
  facet.sort = TRUE,
  x.complete = NULL,
  category.complete = NULL,
  facet.complete = NULL,
  datalabels = TRUE,
  datalabels.round = ifelse(y.percent, 2, 1),
  datalabels.format = "%n",
  datalabels.colour = "grey25",
  datalabels.colour_fill = NULL,
  datalabels.size = (3 * text_factor),
  datalabels.angle = 0,
  datalabels.lineheight = 1,
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  summarise_function = base::sum,
  stacked = FALSE,
  stackedpercent = FALSE,
  horizontal = FALSE,
  reverse = horizontal,
  smooth = NULL,
  smooth.method = NULL,
  smooth.formula = NULL,
  smooth.se = TRUE,
  smooth.level = 0.95,
  smooth.alpha = 0.25,
  smooth.linewidth = 0.75,
  smooth.linetype = 3,
  smooth.colour = NULL,
  size = NULL,
  linetype = 1,
  linewidth = NULL,
  binwidth = NULL,
  width = NULL,
  jitter_seed = NA,
  violin_scale = "count",
  legend.position = NULL,
  legend.title = NULL,
  legend.reverse = FALSE,
  legend.barheight = 6,
  legend.barwidth = 1.5,
  legend.nbin = 300,
  legend.italic = FALSE,
  sankey.node_width = 0.15,
  sankey.node_whitespace = 0.03,
  sankey.alpha = 0.5,
  sankey.remove_axes = NULL,
  zoom = FALSE,
  sep = " / ",
  print = FALSE,
  text_factor = 1,
  font = getOption("plot2.font"),
  theme = getOption("plot2.theme", "theme_minimal2"),
  background = getOption("plot2.colour_background", "white"),
  markdown = TRUE,
  ...
)

## S3 method for class 'sf'
plot2(
  .data,
  x = NULL,
  y = NULL,
  category = NULL,
  facet = NULL,
  type = NULL,
  x.title = FALSE,
  y.title = FALSE,
  category.title = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  title.linelength = 60,
  title.colour = getOption("plot2.colour_font_primary", "black"),
  subtitle.linelength = 60,
  subtitle.colour = getOption("plot2.colour_font_secondary", "grey35"),
  na.replace = "",
  na.rm = FALSE,
  facet.position = "top",
  facet.fill = NULL,
  facet.bold = TRUE,
  facet.italic = FALSE,
  facet.size = 10,
  facet.margin = 8,
  facet.repeat_lbls_x = TRUE,
  facet.repeat_lbls_y = NULL,
  facet.fixed_y = NULL,
  facet.fixed_x = NULL,
  facet.drop = FALSE,
  facet.nrow = NULL,
  facet.relative = FALSE,
  x.date_breaks = NULL,
  x.date_labels = NULL,
  x.date_remove_years = NULL,
  category.focus = NULL,
  colour = getOption("plot2.colour_sf", "grey50"),
  colour_fill = getOption("plot2.colour_sf_fill", getOption("plot2.colour", "ggplot2")),
  colour_opacity = 0,
  x.lbl_angle = 0,
  x.lbl_align = NULL,
  x.lbl_italic = FALSE,
  x.lbl_taxonomy = FALSE,
  x.remove = FALSE,
  x.position = "bottom",
  x.max_items = Inf,
  x.max_txt = "(rest, x%n)",
  category.max_items = Inf,
  category.max_txt = "(rest, x%n)",
  facet.max_items = Inf,
  facet.max_txt = "(rest, x%n)",
  x.breaks = NULL,
  x.n_breaks = NULL,
  x.transform = "identity",
  x.expand = 0,
  x.limits = NULL,
  x.labels = NULL,
  x.character = NULL,
  x.drop = FALSE,
  x.mic = FALSE,
  x.zoom = FALSE,
  y.remove = FALSE,
  y.24h = FALSE,
  y.age = FALSE,
  y.scientific = NULL,
  y.percent = FALSE,
  y.percent_break = 0.1,
  y.breaks = NULL,
  y.n_breaks = NULL,
  y.limits = NULL,
  y.labels = NULL,
  y.expand = 0,
  y.transform = "identity",
  y.position = "left",
  y.zoom = FALSE,
  y_secondary = NULL,
  y_secondary.type = type,
  y_secondary.title = TRUE,
  y_secondary.colour = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.colour_fill = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.scientific = NULL,
  y_secondary.percent = FALSE,
  y_secondary.labels = NULL,
  category.labels = NULL,
  category.percent = FALSE,
  category.breaks = NULL,
  category.limits = NULL,
  category.expand = 0,
  category.midpoint = NULL,
  category.transform = "identity",
  category.date_breaks = NULL,
  category.date_labels = NULL,
  category.character = NULL,
  x.sort = NULL,
  category.sort = TRUE,
  facet.sort = TRUE,
  x.complete = NULL,
  category.complete = NULL,
  facet.complete = NULL,
  datalabels = TRUE,
  datalabels.round = ifelse(y.percent, 2, 1),
  datalabels.format = NULL,
  datalabels.colour = "black",
  datalabels.colour_fill = NULL,
  datalabels.size = (3 * text_factor),
  datalabels.angle = 0,
  datalabels.lineheight = 1,
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  summarise_function = base::sum,
  stacked = FALSE,
  stackedpercent = FALSE,
  horizontal = FALSE,
  reverse = horizontal,
  smooth = NULL,
  smooth.method = NULL,
  smooth.formula = NULL,
  smooth.se = TRUE,
  smooth.level = 0.95,
  smooth.alpha = 0.25,
  smooth.linewidth = 0.75,
  smooth.linetype = 3,
  smooth.colour = NULL,
  size = NULL,
  linetype = 1,
  linewidth = NULL,
  binwidth = NULL,
  width = NULL,
  jitter_seed = NA,
  violin_scale = "count",
  legend.position = "right",
  legend.title = NULL,
  legend.reverse = FALSE,
  legend.barheight = 6,
  legend.barwidth = 1.5,
  legend.nbin = 300,
  legend.italic = FALSE,
  sankey.node_width = 0.15,
  sankey.node_whitespace = 0.03,
  sankey.alpha = 0.5,
  sankey.remove_axes = NULL,
  zoom = FALSE,
  sep = " / ",
  print = FALSE,
  text_factor = 1,
  font = getOption("plot2.font"),
  theme = theme_minimal2(panel.grid.major = element_blank(), panel.grid.minor =
    element_blank(), panel.border = element_blank(), plot.margin = unit(c(5, 5, 0, 0),
    units = "pt"), axis.title = element_blank(), axis.text = element_blank(), axis.line =
    element_blank(), axis.ticks = element_blank()),
  background = getOption("plot2.colour_background", "white"),
  markdown = TRUE,
  data = NULL,
  crs = NULL,
  datalabels.centroid = NULL,
  ...
)

## S3 method for class 'data.frame'
plot2(
  .data,
  x = NULL,
  y = NULL,
  category = NULL,
  facet = NULL,
  type = NULL,
  x.title = TRUE,
  y.title = TRUE,
  category.title = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  title.linelength = 60,
  title.colour = getOption("plot2.colour_font_primary", "black"),
  subtitle.linelength = 60,
  subtitle.colour = getOption("plot2.colour_font_secondary", "grey35"),
  na.replace = "",
  na.rm = FALSE,
  facet.position = "top",
  facet.fill = NULL,
  facet.bold = TRUE,
  facet.italic = FALSE,
  facet.size = 10,
  facet.margin = 8,
  facet.repeat_lbls_x = TRUE,
  facet.repeat_lbls_y = NULL,
  facet.fixed_y = NULL,
  facet.fixed_x = NULL,
  facet.drop = FALSE,
  facet.nrow = NULL,
  facet.relative = FALSE,
  x.date_breaks = NULL,
  x.date_labels = NULL,
  x.date_remove_years = NULL,
  category.focus = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  colour_fill = NULL,
  colour_opacity = 0,
  x.lbl_angle = 0,
  x.lbl_align = NULL,
  x.lbl_italic = FALSE,
  x.lbl_taxonomy = FALSE,
  x.remove = FALSE,
  x.position = "bottom",
  x.max_items = Inf,
  x.max_txt = "(rest, x%n)",
  category.max_items = Inf,
  category.max_txt = "(rest, x%n)",
  facet.max_items = Inf,
  facet.max_txt = "(rest, x%n)",
  x.breaks = NULL,
  x.n_breaks = NULL,
  x.transform = "identity",
  x.expand = NULL,
  x.limits = NULL,
  x.labels = NULL,
  x.character = NULL,
  x.drop = FALSE,
  x.mic = FALSE,
  x.zoom = FALSE,
  y.remove = FALSE,
  y.24h = FALSE,
  y.age = FALSE,
  y.scientific = NULL,
  y.percent = FALSE,
  y.percent_break = 0.1,
  y.breaks = NULL,
  y.n_breaks = NULL,
  y.limits = NULL,
  y.labels = NULL,
  y.expand = NULL,
  y.transform = "identity",
  y.position = "left",
  y.zoom = FALSE,
  y_secondary = NULL,
  y_secondary.type = type,
  y_secondary.title = TRUE,
  y_secondary.colour = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.colour_fill = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.scientific = NULL,
  y_secondary.percent = FALSE,
  y_secondary.labels = NULL,
  category.labels = NULL,
  category.percent = FALSE,
  category.breaks = NULL,
  category.limits = NULL,
  category.expand = 0,
  category.midpoint = NULL,
  category.transform = "identity",
  category.date_breaks = NULL,
  category.date_labels = NULL,
  category.character = NULL,
  x.sort = NULL,
  category.sort = TRUE,
  facet.sort = TRUE,
  x.complete = NULL,
  category.complete = NULL,
  facet.complete = NULL,
  datalabels = TRUE,
  datalabels.round = ifelse(y.percent, 2, 1),
  datalabels.format = "%n",
  datalabels.colour = "grey25",
  datalabels.colour_fill = NULL,
  datalabels.size = (3 * text_factor),
  datalabels.angle = 0,
  datalabels.lineheight = 1,
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  summarise_function = base::sum,
  stacked = FALSE,
  stackedpercent = FALSE,
  horizontal = FALSE,
  reverse = horizontal,
  smooth = NULL,
  smooth.method = NULL,
  smooth.formula = NULL,
  smooth.se = TRUE,
  smooth.level = 0.95,
  smooth.alpha = 0.25,
  smooth.linewidth = 0.75,
  smooth.linetype = 3,
  smooth.colour = NULL,
  size = NULL,
  linetype = 1,
  linewidth = NULL,
  binwidth = NULL,
  width = NULL,
  jitter_seed = NA,
  violin_scale = "count",
  legend.position = NULL,
  legend.title = NULL,
  legend.reverse = FALSE,
  legend.barheight = 6,
  legend.barwidth = 1.5,
  legend.nbin = 300,
  legend.italic = FALSE,
  sankey.node_width = 0.15,
  sankey.node_whitespace = 0.03,
  sankey.alpha = 0.5,
  sankey.remove_axes = NULL,
  zoom = FALSE,
  sep = " / ",
  print = FALSE,
  text_factor = 1,
  font = getOption("plot2.font"),
  theme = getOption("plot2.theme", "theme_minimal2"),
  background = getOption("plot2.colour_background", "white"),
  markdown = TRUE,
  ...
)

## S3 method for class 'matrix'
plot2(
  .data,
  x = NULL,
  y = NULL,
  category = NULL,
  facet = NULL,
  type = NULL,
  x.title = FALSE,
  y.title = FALSE,
  category.title = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  title.linelength = 60,
  title.colour = getOption("plot2.colour_font_primary", "black"),
  subtitle.linelength = 60,
  subtitle.colour = getOption("plot2.colour_font_secondary", "grey35"),
  na.replace = "",
  na.rm = FALSE,
  facet.position = "top",
  facet.fill = NULL,
  facet.bold = TRUE,
  facet.italic = FALSE,
  facet.size = 10,
  facet.margin = 8,
  facet.repeat_lbls_x = TRUE,
  facet.repeat_lbls_y = NULL,
  facet.fixed_y = NULL,
  facet.fixed_x = NULL,
  facet.drop = FALSE,
  facet.nrow = NULL,
  facet.relative = FALSE,
  x.date_breaks = NULL,
  x.date_labels = NULL,
  x.date_remove_years = NULL,
  category.focus = NULL,
  colour = getOption("plot2.colour", "ggplot2"),
  colour_fill = NULL,
  colour_opacity = 0,
  x.lbl_angle = 0,
  x.lbl_align = NULL,
  x.lbl_italic = FALSE,
  x.lbl_taxonomy = FALSE,
  x.remove = FALSE,
  x.position = "bottom",
  x.max_items = Inf,
  x.max_txt = "(rest, x%n)",
  category.max_items = Inf,
  category.max_txt = "(rest, x%n)",
  facet.max_items = Inf,
  facet.max_txt = "(rest, x%n)",
  x.breaks = NULL,
  x.n_breaks = NULL,
  x.transform = "identity",
  x.expand = NULL,
  x.limits = NULL,
  x.labels = NULL,
  x.character = NULL,
  x.drop = FALSE,
  x.mic = FALSE,
  x.zoom = FALSE,
  y.remove = FALSE,
  y.24h = FALSE,
  y.age = FALSE,
  y.scientific = NULL,
  y.percent = FALSE,
  y.percent_break = 0.1,
  y.breaks = NULL,
  y.n_breaks = NULL,
  y.limits = NULL,
  y.labels = NULL,
  y.expand = NULL,
  y.transform = "identity",
  y.position = "left",
  y.zoom = FALSE,
  y_secondary = NULL,
  y_secondary.type = type,
  y_secondary.title = TRUE,
  y_secondary.colour = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.colour_fill = get_colour(getOption("plot2.colour", "ggplot2"), 2),
  y_secondary.scientific = NULL,
  y_secondary.percent = FALSE,
  y_secondary.labels = NULL,
  category.labels = NULL,
  category.percent = FALSE,
  category.breaks = NULL,
  category.limits = NULL,
  category.expand = 0,
  category.midpoint = NULL,
  category.transform = "identity",
  category.date_breaks = NULL,
  category.date_labels = NULL,
  category.character = NULL,
  x.sort = NULL,
  category.sort = TRUE,
  facet.sort = TRUE,
  x.complete = NULL,
  category.complete = NULL,
  facet.complete = NULL,
  datalabels = TRUE,
  datalabels.round = ifelse(y.percent, 2, 1),
  datalabels.format = "%n",
  datalabels.colour = "grey25",
  datalabels.colour_fill = NULL,
  datalabels.size = (3 * text_factor),
  datalabels.angle = 0,
  datalabels.lineheight = 1,
  decimal.mark = dec_mark(),
  big.mark = big_mark(),
  summarise_function = base::sum,
  stacked = FALSE,
  stackedpercent = FALSE,
  horizontal = FALSE,
  reverse = horizontal,
  smooth = NULL,
  smooth.method = NULL,
  smooth.formula = NULL,
  smooth.se = TRUE,
  smooth.level = 0.95,
  smooth.alpha = 0.25,
  smooth.linewidth = 0.75,
  smooth.linetype = 3,
  smooth.colour = NULL,
  size = NULL,
  linetype = 1,
  linewidth = NULL,
  binwidth = NULL,
  width = NULL,
  jitter_seed = NA,
  violin_scale = "count",
  legend.position = NULL,
  legend.title = NULL,
  legend.reverse = FALSE,
  legend.barheight = 6,
  legend.barwidth = 1.5,
  legend.nbin = 300,
  legend.italic = FALSE,
  sankey.node_width = 0.15,
  sankey.node_whitespace = 0.03,
  sankey.alpha = 0.5,
  sankey.remove_axes = NULL,
  zoom = FALSE,
  sep = " / ",
  print = FALSE,
  text_factor = 1,
  font = getOption("plot2.font"),
  theme = getOption("plot2.theme", "theme_minimal2"),
  background = getOption("plot2.colour_background", "white"),
  markdown = TRUE,
  ...
)

Arguments

.data, data	data to plot
x	plotting 'direction' for the x axis. This can be: A single variable from .data, such as x = column1 A function to calculate over one or more variables from .data, such as x = format(column1, "%Y"), or x = ifelse(column1 == "A", "Group A", "Other") Multiple variables from .data, such as x = c(column1, column2, column2), or using selection helpers such as x = where(is.character) or x = starts_with("var_") (only allowed and required for Sankey plots using type = "sankey")
y	values to use for plotting along the y axis. This can be: A single variable from .data, such as y = column1 Multiple variables from .data, such as y = c(column1, column2) or y = c(name1 = column1, "name 2" = column2), or using selection helpers such as y = where(is.double) or y = starts_with("var_") (multiple variables only allowed if category is not set) A function to calculate over .data returning a single value, such as y = n() for the row count, or based on other variables such as y = n_distinct(person_id), y = max(column1), or y = median(column2) / column3 A function to calculate over .data returning multiple values, such as y = quantile(column1, c(0.25, 0.75)) or y = range(age) (multiple values only allowed if category is not set)
category, facet	plotting 'direction' (category is called 'fill' and 'colour' in ggplot2). This can be: A single variable from .data, such as category = column1 A function to calculate over one or more variables from .data, such as category = median(column2) / column3, or facet = ifelse(column1 == "A", "Group A", "Other") Multiple variables from .data, such as facet = c(column1, column2) (use sep to control the separator character) One or more variables from .data using selection helpers, such as category = where(is.double) or facet = starts_with("var_") The category can also be a date or date/time (class Date or POSIXt).
type, y_secondary.type	type of visualisation to use. This can be: A ggplot2 geom name or their abbreviation such as "col" and "point". All geoms are supported (including geom_blank()). Full function names can be used (e.g., "geom_histogram"), but they can also be abbreviated (e.g., "h", "hist"). The following geoms can be abbreviated by their first character: area ("a"), boxplot ("b"), column ("c"), histogram ("h"), jitter ("j"), line ("l"), point ("p"), ribbon ("r"), and violin ("v"). Please note: in ggplot2, 'bars' and 'columns' are equal, while it is common to many people that 'bars' are oriented horizontally and 'columns' are oriented vertically since Microsoft Excel has been using these terms this way for many years. For this reason, type = "bar" will set type = "col" and horizontal = TRUE. One of these additional types: "barpercent" (short: "bp"), which is effectively a shortcut to set type = "col" and horizontal = TRUE and x.max_items = 10 and x.sort = "freq-desc" and datalabels.format = "%n (%p)". "linedot" (short: "ld"), which sets type = "line" and adds two point geoms using add_point(); one with large white dots and one with smaller dots using the colours set in colour. This is essentially equal to base R plot(..., type = "b") but with closed shapes. "dumbbell" (short: "d"), which sets type = "point" and horizontal = TRUE, and adds a line between the points (using geom_segment()). The line colour cannot be changed. This plot type is only possible when the category has two distinct values. "sankey" (short: "s") creates a Sankey plots using category for the flows and requires x to contain multiple variables from .data. At default, it also sets x.expand = c(0.05, 0.05) and y.limits = c(NA, NA) and y.expand = c(0.01, 0.01). The so-called 'nodes' (the 'blocks' with text) are considered the datalabels, so you can set the text size and colour of the nodes using datalabels.size, datalabels.colour, and datalabels.colour_fill. The transparency of the flows can be set using sankey.alpha, and the width of the nodes can be set using sankey.node_width. Sankey plots can also be flipped using horizontal = TRUE. Left blank. In this case, the type will be determined automatically: "boxplot" if there is no x axis or if the length of unique values per x axis item is at least 3, "point" if both the y and x axes are numeric, and the option "plot2.default_type" otherwise (which defaults to "col"). Use type = "blank" or type = "geom_blank" to not add a geom.
title, subtitle, caption, tag, x.title, y.title, category.title, legend.title, y_secondary.title	a title to use. This can be: A character, which supports markdown by using md_to_expression() internally if markdown = TRUE (which is the default) A function to calculate over .data, such as title = paste("Based on n =", n_distinct(person_id), "individuals") or subtitle = paste("Total rows:", n()), see Examples An expression, e.g. using parse(text = "...") The category.title defaults to TRUE if the legend items are numeric.
title.linelength	maximum number of characters per line in the title, before a linebreak occurs
title.colour	text colour of the title
subtitle.linelength	maximum number of characters per line in the subtitle, before a linebreak occurs
subtitle.colour	text colour of the subtitle
na.replace	character to put in place of NA values if na.rm = FALSE
na.rm	remove NA values from showing in the plot
facet.position, facet.fill, facet.bold, facet.italic, facet.size, facet.margin, facet.repeat_lbls_x, facet.repeat_lbls_y, facet.drop, facet.nrow, facet.relative	additional settings for the plotting direction facet
facet.fixed_y	a logical to indicate whether all y scales should have the same limits. Defaults to TRUE only if the coefficient of variation (standard deviation divided by mean) of the maximum values of y is less than 25%.
facet.fixed_x	a logical to indicate whether all x scales should have the same breaks. This acts like the inverse of x.drop.
x.date_breaks	breaks to use when the x axis contains dates, will be determined automatically if left blank. This accepts values such as "1 day" and "2 years".
x.date_labels	labels to use when the x axis contains dates, will be determined automatically if left blank. This accepts 'Excel' date-language such as "d mmmm yyyy".
x.date_remove_years	a logical to indicate whether the years of all x values must be unified. This will set the years of all x values to 1970 if the data does not contain a leap year, and to 1972 otherwise. This allows to plot years on the category while maintaining a date range on x. The default is FALSE, unless category contains all years present in x.
category.focus	a value of category that should be highlighted, meaning that all other values in category will be greyed out. This can also be a numeric value between 1 and the length of unique values of category, e.g. category.focus = 2 to focus on the second legend item.
colour	get_colour(s) to set, will be evaluated with get_colour() if set. This can also be one of the viridis colours with automatic implementation for any plot: "viridis", "magma", "inferno", "plasma", "cividis", "rocket", "mako" or "turbo". Also, this can also be a named vector to match values of category, see Examples. Using a named vector can also be used to manually sort the values of category.
colour_fill	get_colour(s) to be used for filling, will be determined automatically if left blank and will be evaluated with get_colour()
colour_opacity	amount of opacity for colour/colour_fill (0 = solid, 1 = transparent)
x.lbl_angle	angle to use for the x axis in a counter-clockwise direction (i.e., a value of 90 will orient the axis labels from bottom to top, a value of 270 will orient the axis labels from top to bottom)
x.lbl_align	alignment for the x axis between 0 (left aligned) and 1 (right aligned)
x.lbl_italic	logical to indicate whether the x labels should in in italics
x.lbl_taxonomy	a logical to transform all words of the x labels into italics that are in the microorganisms data set of the AMR package. This uses md_to_expression() internally and will set x.labels to parse expressions.
x.remove, y.remove	a logical to indicate whether the axis labels and title should be removed
x.position, y.position	position of the axis
x.max_items, category.max_items, facet.max_items	number of maximum items to use, defaults to infinite. All other values will be grouped and summarised using the summarise_function function. Please note: the sorting will be applied first, allowing to e.g. plot the top n most frequent values of the x axis by combining x.sort = "freq-desc" with ⁠x.max_items =⁠ n.
x.max_txt, category.max_txt, facet.max_txt	the text to use of values not included number of ⁠*.max_items⁠. The placeholder ⁠%n⁠ will be replaced with the outcome of the summarise_function function, the placeholder ⁠%p⁠ will be replaced with the percentage.
x.breaks, y.breaks	a breaks function or numeric vector to use for the axis
x.n_breaks, y.n_breaks	number of breaks, only useful if x.breaks cq. y.breaks is NULL
x.transform, y.transform, category.transform	a transformation function to use, e.g. "log2". This can be: "asinh", "asn", "atanh", "boxcox", "compose", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt", "time", "timespan", "yj".
x.expand, y.expand	expansion to use for the axis, can be length 1 or 2. x.expand defaults to 0.5 and y.expand defaults to 0.25, except for sf objects (then both default to 0).
x.limits, y.limits	limits to use for the axis, can be length 1 or 2. Use NA for the highest or lowest value in the data, e.g. y.limits = c(0, NA) to have the y scale start at zero.
x.labels, y.labels, y_secondary.labels	a labels function or character vector to use for the axis
x.character	a logical to indicate whether the values of the x axis should be forced to character. The default is FALSE, except for years (values between 2000 and 2050) and months (values from 1 to 12).
x.drop	logical to indicate whether factor levels should be dropped
x.mic	logical to indicate whether the x axis should be formatted as MIC values, by dropping all factor levels and adding missing factors of 2
x.zoom, y.zoom	a logical to indicate if the axis should be zoomed on the data, by setting x.limits = c(NA, NA) and x.expand = 0 for the x axis, or y.limits = c(NA, NA) and y.expand = 0 for the y axis
y.24h	a logical to indicate whether the y labels and breaks should be formatted as 24-hour sequences
y.age	a logical to indicate whether the y labels and breaks should be formatted as ages in years
y.scientific, y_secondary.scientific	a logical to indicate whether the y labels should be formatted in scientific notation. Defaults to TRUE only if the range of the y values spans more than 10e5.
y.percent, y_secondary.percent	a logical to indicate whether the y labels should be formatted as percentages
y.percent_break	a value on which the y axis should have breaks
y_secondary	values to use for plotting along the secondary y axis. This functionality is poorly supported by ggplot2 and might give unexpected results. Setting the secondary y axis will set the colour to the axis titles.
y_secondary.colour, y_secondary.colour_fill	colours to set for the secondary y axis, will be evaluated with get_colour()
category.labels, category.percent, category.breaks, category.expand, category.midpoint	settings for the plotting direction category.
category.limits	limits to use for a numeric category, can be length 1 or 2. Use NA for the highest or lowest value in the data, e.g. category.limits = c(0, NA) to have the scale start at zero.
category.date_breaks	breaks to use when the category contains dates, will be determined automatically if left blank. This will be passed on to seq.Date(by = ...) and thus can be: a number, taken to be in days, or a character string containing one of "day", "week", "month", "quarter" or "year" (optionally preceded by an integer and a space, and/or followed by "s").
category.date_labels	labels to use when the category contains dates, will be determined automatically if left blank. This accepts 'Excel' date-language such as "d mmmm yyyy".
category.character	a logical to indicate whether the values of the category should be forced to character. The default is FALSE, except for years (values between 2000 and 2050) and months (values from 1 to 12).
x.sort, category.sort, facet.sort	sorting of the plotting direction, defaults to TRUE, except for continuous values on the x axis (such as dates and numbers). Applying one of the sorting methods will transform the values to an ordered factor, which ggplot2 uses to orient the data. Valid values are: A manual vector of values TRUE: sort factors on their levels, otherwise sort ascending on alphabet, while maintaining numbers in the text (numeric sort) FALSE: sort according to the order in the data NULL: do not sort/transform at all "asc" or "alpha": sort as TRUE "desc": sort factors on their reversed levels, otherwise sort descending on alphabet, while maintaining numbers in the text (numeric sort) "order" or "inorder": sort as FALSE "freq" or "freq-desc": sort descending according to the frequencies of y computed by summarise_function (highest value first) "freq-asc": sort ascending according to the frequencies of y computed by summarise_function (lowest value first)
x.complete, category.complete, facet.complete	a value to complete the data. This makes use of tidyr::full_seq() and tidyr::complete(). For example, using x.complete = 0 will apply data |> complete(full_seq(x, ...), fill = list(x = 0)). Using value TRUE (e.g., x.complete = TRUE) is identical to using value 0.
datalabels	values to show as datalabels, see also datalabels.format. This can be: Left blank. This will default to the values of y in column-type plots, or when plotting spatial 'sf' data, the values of the first column. It will print a maximum of 25 labels unless datalabels = TRUE. TRUE or FALSE to force or remove datalabels A function to calculate over .data, such as datalabels = paste(round(column1), "\n", column2)
datalabels.round	number of digits to round the datalabels, applies to both "%n" and "%p" for replacement (see datalabels.format)
datalabels.format	format to use for datalabels. This can be a function (such as euros()) or a text. For the text, "%n" will be replaced by the count number, and "%p" will be replaced by the percentage of the total count. Use datalabels.format = NULL to not transform the datalabels.
datalabels.colour, datalabels.colour_fill, datalabels.size, datalabels.angle, datalabels.lineheight	settings for the datalabels
decimal.mark	decimal mark, defaults to dec_mark()
big.mark	thousands separator, defaults to big_mark()
summarise_function	a function to use if the data has to be summarised, see Examples. This can also be NULL, which will be converted to function(x) x.
stacked	a logical to indicate that values must be stacked
stackedpercent	a logical to indicate that values must be 100% stacked
horizontal	a logical to turn the plot 90 degrees using coord_flip(). This option also updates some theme options, so that e.g., x.lbl_italic will still apply to the original x axis.
reverse	a logical to reverse the values of category. Use legend.reverse to reverse the legend of category.
smooth	a logical to add a smooth. In histograms, this will add the density count as an overlaying line (default: TRUE). In all other cases, a smooth will be added using geom_smooth() (default: FALSE).
smooth.method, smooth.formula, smooth.se, smooth.level, smooth.alpha, smooth.linewidth, smooth.linetype, smooth.colour	settings for smooth
size	size of the geom. Defaults to 2 for geoms point and jitter, 5 for a dumbbell plots (using type = "dumbbell"), and to 0.75 otherwise.
linetype	linetype of the geom, only suitable for geoms that draw lines. Defaults to 1.
linewidth	linewidth of the geom, only suitable for geoms that draw lines. Defaults to: 0.5 for geoms that have no area (such as line), and for geoms boxplot/violin 0.1 for sf 0.25 for geoms that are continous and have fills (such as area) 1.0 for dumbbell plots (using type = "dumbbell") 0.5 otherwise (such as histogram and area)
binwidth	width of bins (only useful for geom = "histogram"), can be specified as a numeric value or as a function that calculates width from x, see geom_histogram(). It defaults to approx. diff(range(x)) divided by 12 to 22 based on the data.
width	width of the geom. Defaults to 0.75 for geoms boxplot, violin and jitter, and to 0.5 otherwise.
jitter_seed	seed (randomisation factor) to be set when using type = "jitter"
violin_scale	scale to be set when using type = "violin", can also be set to "area"
legend.position	position of the legend, must be "top", "right", "bottom", "left" or "none" (or NA or NULL), can be abbreviated. Defaults to "right" for numeric category values and 'sf' plots, and "top" otherwise.
legend.reverse, legend.barheight, legend.barwidth, legend.nbin, legend.italic	other settings for the legend
sankey.node_width	width of the vertical nodes in a Sankey plot (i.e., when type = "sankey")
sankey.node_whitespace	whitespace between the nodes
sankey.alpha	alpha of the flows in a Sankey plot (i.e., when type = "sankey")
sankey.remove_axes	logical to indicate whether all axes must be removed in a Sankey plot (i.e., when type = "sankey")
zoom	a logical to indicate if the plot should be scaled to the data, i.e., not having the x and y axes to start at 0. This will set x.zoom = TRUE and y.zoom = TRUE.
sep	separator character to use if multiple columns are given to either of the three directions: x, category and facet, e.g. facet = c(column1, column2)
print	a logical to indicate if the result should be printed instead of just returned
text_factor	text factor to use, which will apply to all texts shown in the plot
font	font (family) to use, can be set with options(plot2.font = "..."). Can be any installed system font or any of the > 1400 font names from Google Fonts. When using custom fonts in R Markdown, be sure to set the chunk option fig.showtext = TRUE, otherwise an informative error will be generated.
theme	a valid ggplot2 theme to apply, or NULL to use the default theme_grey(). This argument accepts themes (e.g., theme_bw()), functions (e.g., theme_bw) and characters themes (e.g., "theme_bw"). The default is theme_minimal2(), but can be set with options(plot2.theme = "...").
background	the background colour of the entire plot, can also be NA to remove it. Will be evaluated with get_colour(). Only applies when theme is not NULL.
markdown	a logical to turn all labels and titles into plotmath expressions, by converting common markdown language using the md_to_expression() function (defaults to TRUE)
...	any argument to give to the geom. This will override automatically-set settings for the geom.
crs	the coordinate reference system (CRS) to use. If this is not left blank, sf::st_transform() will be used to transform the geometric data to the new CRS.
datalabels.centroid	a logical to indicate whether datalabels must be centred on the polygon (using sf::st_centroid(), the default), or be placed on the 'best' spot on the surface (using sf::st_point_on_surface())

Details

For geographic information system (GIS) analysis, use the sf package with a data set containing geometries. The result can be used as input for plot2().

---

An Even More Minimal Theme

Description

This ggplot2 theme provides even more white area and less clutter than theme_minimal().

Usage

theme_minimal2(
  ...,
  colour_font_primary = getOption("plot2.colour_font_primary", "black"),
  colour_font_secondary = getOption("plot2.colour_font_secondary", "grey35"),
  colour_font_axis = getOption("plot2.colour_font_axis", "grey25"),
  colour_background = getOption("plot2.colour_background", "white")
)

Arguments

...	arguments passed on to ggplot2::theme()
colour_font_primary	colour to set for the plot title and tag
colour_font_secondary	colour to set for the plot subtitle and caption
colour_font_axis	colour to set for the axis titles on both x and y
colour_background	colour to set for the background

Examples

library(ggplot2)
ggplot(mtcars, aes(hp, mpg)) +
  geom_point()
  
ggplot(mtcars, aes(hp, mpg)) +
  geom_point() +
  theme_minimal2()
  
# in plot2(), the 'theme' argument defaults to theme_minimal2():
mtcars |>
  plot2(hp, mpg)
  
# set to NULL to use the ggplot2 default:
mtcars |>
  plot2(hp, mpg, theme = NULL)

---