Package 'ggvenn'

Utility functions for data type conversion between data.frame and list.

Description

Utility functions for data type conversion between data.frame and list.

Usage

data_frame_to_list(x)

list_to_data_frame(x)

Arguments

x	A data.frame with logical columns representing sets, or a list of sets.

Value

A list of sets or a data.frame with logical columns representing sets.

Examples

# Convert data.frame to list
d <- dplyr::tibble(name = 1:6,
            A = c(rep(TRUE, 5), FALSE),
            B = rep(c(FALSE, TRUE), each = 3))
print(d)
data_frame_to_list(d)

# Convert list to data.frame
a <- list(A = 1:5, B = 4:6)
print(a)
list_to_data_frame(a)

# Round-trip conversion
identical(a, data_frame_to_list(list_to_data_frame(a)))  # TRUE
identical(d, list_to_data_frame(data_frame_to_list(d)))  # TRUE

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Plot venn diagram as a ggplot layer object. It supports only data frame as input.

Description

Plot venn diagram as a ggplot layer object. It supports only data frame as input.

Usage

geom_venn(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  set_names = NULL,
  element_column = NULL,
  show_elements = FALSE,
  show_set_totals = "none",
  show_stats = c("cp", "c", "p"),
  show_counts = TRUE,
  show_percentage = TRUE,
  digits = 1,
  label_sep = ",",
  count_column = NULL,
  show_outside = c("auto", "none", "always"),
  auto_scale = FALSE,
  fill_color = default_color_list,
  fill_alpha = 0.5,
  stroke_color = "black",
  stroke_alpha = 1,
  stroke_size = 1,
  stroke_linetype = "solid",
  set_name_color = "black",
  set_name_size = 6,
  text_color = "black",
  text_size = 4,
  comma_sep = FALSE,
  padding = 0.2,
  max_elements = 6,
  text_truncate = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	A data.frame or a list as input data.
stat	The statistical transformation to use on the data for this layer, as a string.
position	A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following: The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position. A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter". For more information and other ways to specify the position, see the layer position documentation.
...	Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored. Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data. When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept. Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept. The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.
set_names	Set names, use column names if omitted.
element_column	A single character value use as column name to select elements.
show_elements	Show set elements instead of count/percentage.
show_set_totals	Show total count (c) and/or percentage (p) for each set. Pass a string like "cp" to show both. Any other string like "none" to hide both.
show_stats	Show count (c) and/or percentage (p) for each set. Pass a string like "cp" to show both.
show_counts	Show count for each set.
show_percentage	Show percentage for each set.
digits	The desired number of digits after the decimal point.
label_sep	Separator character for displaying elements.
count_column	Specify column for element repeat count.
show_outside	Show outside elements (not belongs to any set). Options: "auto", "none", "always".
auto_scale	Allow automatically resizing circles according to element counts (only for 2-set diagrams).
fill_color	Filling colors in circles. Can be a single color or a vector of colors for each set.
fill_alpha	Transparency for filling circles. Can be a single value or a vector for each set.
stroke_color	Stroke color for drawing circles. Can be a single color or a vector of colors for each set.
stroke_alpha	Transparency for drawing circles. Can be a single value or a vector for each set.
stroke_size	Stroke size for drawing circles. Can be a single value or a vector for each set.
stroke_linetype	Line type for drawing circles. Can be a single value or a vector for each set.
set_name_color	Text color for set names.
set_name_size	Text size for set names.
text_color	Text color for intersect contents.
text_size	Text size for intersect contents.
comma_sep	Whether to use comma as separator for displaying numbers.
padding	Padding for the plot. Change this to allow longer labels to be displayed.
max_elements	Maximum number of elements to display when show_elements=TRUE.
text_truncate	Whether to truncate text when elements exceed max_elements.

Value

A ggplot layer object to add to a ggplot.

See Also

ggvenn

Examples

library(ggvenn)

# use data.frame as input
d <- dplyr::tibble(
  value   = c(1,     2,     3,     5,     6,     7,     8,     9),
  `Set 1` = c(TRUE,  FALSE, TRUE,  TRUE,  FALSE, TRUE,  FALSE, TRUE),
  `Set 2` = c(TRUE,  FALSE, FALSE, TRUE,  FALSE, FALSE, FALSE, TRUE),
  `Set 3` = c(TRUE,  TRUE,  FALSE, FALSE, FALSE, FALSE, TRUE,  TRUE),
  `Set 4` = c(FALSE, FALSE, FALSE, FALSE, TRUE,  TRUE,  FALSE, FALSE)
)

# ggplot gramma
ggplot(d) +
  geom_venn(aes(A = `Set 1`, B = `Set 2`)) +
  coord_fixed() +
  theme_void()
ggplot(d) +
  geom_venn(aes(A = `Set 1`, B = `Set 2`, C = `Set 3`)) +
  coord_fixed() +
theme_void()
ggplot(d) +
  geom_venn(aes(A = `Set 1`, B = `Set 2`, C = `Set 3`, D = `Set 4`)) +
  coord_fixed() +
  theme_void()

# set fill color
ggplot(d) +
  geom_venn(aes(A = `Set 1`, B = `Set 2`), fill_color = c("red", "blue")) +
  coord_fixed() +
  theme_void()

# hide percentage
ggplot(d) +
  geom_venn(aes(A = `Set 1`, B = `Set 2`), show_stats = "c") +
  coord_fixed() +
  theme_void()

# change precision of percentages
ggplot(d) +
  geom_venn(aes(A = `Set 1`, B = `Set 2`), digits = 2) +
  coord_fixed() +
  theme_void()

# show elements instead of count/percentage
ggplot(d) +
  geom_venn(aes(A = `Set 1`, B = `Set 2`, C = `Set 3`, D = `Set 4`, label = value)) +
  coord_fixed() +
  theme_void()

---

Extract Venn diagram data table from ggvenn plot

Description

Extract Venn diagram data table from ggvenn plot

Usage

get_venn_table(g)

Arguments

g	A ggplot object created by ggvenn()

Value

A data frame containing the Venn diagram intersection data

Examples

library(ggvenn)
g <- ggvenn(list(A = 1:5, B = 4:9, C = c(2:3, 8:12), D = c(1, 5, 9)))
get_venn_table(g)

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Plot venn diagram as an independent function. It supports both data frame and list as input.

Description

Plot venn diagram as an independent function. It supports both data frame and list as input.

Usage

ggvenn(
  data,
  columns = NULL,
  element_column = NULL,
  show_elements = FALSE,
  show_set_totals = "none",
  show_stats = c("cp", "c", "p"),
  show_counts = TRUE,
  show_percentage = TRUE,
  digits = 1,
  label_sep = ",",
  count_column = NULL,
  show_outside = c("auto", "none", "always"),
  auto_scale = FALSE,
  fill_color = default_color_list,
  fill_alpha = 0.5,
  stroke_color = "black",
  stroke_alpha = 1,
  stroke_size = 1,
  stroke_linetype = "solid",
  set_name_color = "black",
  set_name_size = 6,
  text_color = "black",
  text_size = 4,
  comma_sep = FALSE,
  padding = 0.2,
  max_elements = 6,
  text_truncate = TRUE
)

Arguments

data	A data.frame or a list as input data.
columns	A character vector use as index to select columns/elements.
element_column	A single character value use as column name to select elements. It is only allowed when data is a data.frame.
show_elements	Show set elements instead of count/percentage.
show_set_totals	Show total count (c) and/or percentage (p) for each set. Pass a string like "cp" to show both. Any other string like "none" to hide both.
show_stats	Show count (c) and/or percentage (p) for each set. Pass a string like "cp" to show both. Any other string like "none" to hide both.
show_counts	Show count for each set.
show_percentage	Show percentage for each set.
digits	The desired number of digits after the decimal point.
label_sep	Separator character for displaying elements.
count_column	Specify column for element repeat count.
show_outside	Show outside elements (not belongs to any set). Options: "auto", "none", "always".
auto_scale	Allow automatically resizing circles according to element counts (only for 2-set diagrams).
fill_color	Filling colors in circles. Can be a single color or a vector of colors for each set.
fill_alpha	Transparency for filling circles. Can be a single value or a vector for each set.
stroke_color	Stroke color for drawing circles. Can be a single color or a vector of colors for each set.
stroke_alpha	Transparency for drawing circles. Can be a single value or a vector for each set.
stroke_size	Stroke size for drawing circles. Can be a single value or a vector for each set.
stroke_linetype	Line type for drawing circles. Can be a single value or a vector for each set.
set_name_color	Text color for set names.
set_name_size	Text size for set names.
text_color	Text color for intersect contents.
text_size	Text size for intersect contents.
comma_sep	Whether to use comma as separator for displaying numbers.
padding	Padding for the plot. Change this to allow longer labels to be displayed.
max_elements	Maximum number of elements to display when show_elements=TRUE.
text_truncate	Whether to truncate text when elements exceed max_elements.

Value

The ggplot object to print or save to file.

See Also

geom_venn

Examples

library(ggvenn)

# use list as input
a <- list(A = 1:5, B = 4:9, C = c(2:3, 8:12), D = c(1, 5, 9))
ggvenn(a, c("A", "B"))
ggvenn(a, c("A", "B", "C"))
ggvenn(a)

# use data.frame as input
d <- dplyr::tibble(value   = c(1,     2,     3,     5,     6,     7,     8,     9),
            `Set 1` = c(TRUE,  FALSE, TRUE,  TRUE,  FALSE, TRUE,  FALSE, TRUE),
            `Set 2` = c(TRUE,  FALSE, FALSE, TRUE,  FALSE, FALSE, FALSE, TRUE),
            `Set 3` = c(TRUE,  TRUE,  FALSE, FALSE, FALSE, FALSE, TRUE,  TRUE),
            `Set 4` = c(FALSE, FALSE, FALSE, FALSE, TRUE,  TRUE,  FALSE, FALSE))
ggvenn(d, c("Set 1", "Set 2"))
ggvenn(d, c("Set 1", "Set 2", "Set 3"))
ggvenn(d)

# set fill color
ggvenn(d, c("Set 1", "Set 2"), fill_color = c("red", "blue"))

# hide percentage
ggvenn(d, c("Set 1", "Set 2"), show_stats = "c")

# change precision of percentages
ggvenn(d, c("Set 1", "Set 2"), digits = 2)

# show elements instead of count/percentage
ggvenn(a, show_elements = TRUE)
ggvenn(d, show_elements = TRUE, element_column = "value")

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