ggVennDiagram

https://gaospecial.github.io/ggVennDiagram/
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ggVennDiagram is an R package that creates publication-quality Venn diagrams for 2-7 sets and...
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### Generate Example Data

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-ggVennDiagram.html

Setup script to create a list of gene sets and load required libraries.

```R
genes <- paste0("gene",1:1000)
set.seed(20210302)
gene_list <- list(A = sample(genes,100),
                  B = sample(genes,200),
                  C = sample(genes,300),
                  D = sample(genes,200))

library(ggVennDiagram)
library(ggplot2)
```

--------------------------------

### Install ggVennDiagram

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-ggVennDiagram.html

Commands to install the package from CRAN or the development version from GitHub.

```R
install.packages("ggVennDiagram")
```

```R
# install.packages("devtools")
devtools::install_github("gaospecial/ggVennDiagram")
```

--------------------------------

### Generate example data

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Create a list of gene sets for Venn diagram visualization.

```R
genes <- paste0("gene",1:1000)
set.seed(20231214)
gene_list <- list(A = sample(genes,100),
                  B = sample(genes,200),
                  C = sample(genes,300),
                  D = sample(genes,200))
```

--------------------------------

### Process Venn Data Example

Source: https://gaospecial.github.io/ggVennDiagram/reference/process_data.html

Demonstrates the basic usage of process_data with a Venn object created from a list of sets.

```R
if (FALSE) { # \dontrun{
 venn = Venn(list(A=1:3,B=2:5,C=4:8))
 data = process_data(venn)
} # }
```

--------------------------------

### Calculate set union examples

Source: https://gaospecial.github.io/ggVennDiagram/reference/unite.html

Demonstrates calculating the union of all sets or a subset of sets within a Venn object.

```R
  venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
  unite(venn)
#>  [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o"
  unite(venn, slice = c(1, 2))
#>  [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l"
```

--------------------------------

### Example Usage of Venn Data Processing

Source: https://gaospecial.github.io/ggVennDiagram/reference/venn_data.html

Demonstrates creating a Venn object from a list and processing set and region data.

```R
x = list(
A = sample(letters, 8),
B = sample(letters, 8),
C = sample(letters, 8),
D = sample(letters, 8)
)

venn = Venn(x)
process_set_data(venn)
#> # A tibble: 4 × 4
#>   id    name  item         count
#>   <chr> <chr> <named list> <int>
#> 1 1     A     <chr [8]>        8
#> 2 2     B     <chr [8]>        8
#> 3 3     C     <chr [8]>        8
#> 4 4     D     <chr [8]>        8
process_region_data(venn)
#> # A tibble: 15 × 4
#>    id      name    item      count
#>    <chr>   <chr>   <list>    <int>
#>  1 1       A       <chr [2]>     2
#>  2 2       B       <chr [4]>     4
#>  3 3       C       <chr [3]>     3
#>  4 4       D       <chr [3]>     3
#>  5 1/2     A/B     <chr [1]>     1
#>  6 1/3     A/C     <chr [1]>     1
#>  7 1/4     A/D     <chr [2]>     2
#>  8 2/3     B/C     <chr [1]>     1
#>  9 2/4     B/D     <chr [1]>     1
#> 10 3/4     C/D     <chr [1]>     1
#> 11 1/2/3   A/B/C   <chr [1]>     1
#> 12 1/2/4   A/B/D   <chr [0]>     0
#> 13 1/3/4   A/C/D   <chr [1]>     1
#> 14 2/3/4   B/C/D   <chr [0]>     0
#> 15 1/2/3/4 A/B/C/D <chr [0]>     0
```

--------------------------------

### Apply GNU GPL Source File Header

Source: https://gaospecial.github.io/ggVennDiagram/LICENSE.html

Include this notice at the start of each source file to declare the program's license and warranty exclusion.

```text
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) 2019 Chun-Hui Gao

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
```

--------------------------------

### Create a 4-set Venn Diagram

Source: https://gaospecial.github.io/ggVennDiagram/reference/ggVennDiagram.html

Example of creating a 4-set Venn diagram using the ggVennDiagram function with a list of four sets.

```R
library(ggVennDiagram)
x = list(A=1:5,B=2:7,C=3:6,D=4:9)
ggVennDiagram(x)  # 4d venn
```

--------------------------------

### Create a 2-set Venn Diagram

Source: https://gaospecial.github.io/ggVennDiagram/reference/ggVennDiagram.html

Example of creating a 2-set Venn diagram by subsetting the input list to include only the first two sets.

```R
ggVennDiagram(x[1:2])  # 2d venn
```

--------------------------------

### Create a 3-set Venn Diagram

Source: https://gaospecial.github.io/ggVennDiagram/reference/ggVennDiagram.html

Example of creating a 3-set Venn diagram by subsetting the input list to include only the first three sets.

```R
ggVennDiagram(x[1:3])  # 3d venn
```

--------------------------------

### Get All Shapes

Source: https://gaospecial.github.io/ggVennDiagram/reference/get_shapes.html

Retrieves a tibble containing all available shapes for Venn diagrams.

```APIDOC
## GET /shapes

### Description
Retrieves a tibble containing all available shapes for Venn diagrams.

### Method
GET

### Endpoint
/shapes

### Parameters
None

### Request Body
None

### Response
#### Success Response (200)
- **shape_id** (chr) - Unique identifier for the shape.
- **nsets** (int) - The number of sets the shape is associated with.
- **type** (chr) - The type of shape (e.g., circle, ellipse, polygon, triangle).

#### Response Example
```json
{
  "data": [
    { "shape_id": "101", "nsets": 1, "type": "circle" },
    { "shape_id": "201f", "nsets": 2, "type": "circle" },
    { "shape_id": "201", "nsets": 2, "type": "circle" },
    { "shape_id": "301f", "nsets": 3, "type": "circle" },
    { "shape_id": "301", "nsets": 3, "type": "circle" },
    { "shape_id": "401f", "nsets": 4, "type": "ellipse" },
    { "shape_id": "402", "nsets": 4, "type": "polygon" },
    { "shape_id": "501", "nsets": 5, "type": "polygon" },
    { "shape_id": "502", "nsets": 5, "type": "polygon" },
    { "shape_id": "601t", "nsets": 6, "type": "triangle" },
    { "shape_id": "601", "nsets": 6, "type": "polygon" },
    { "shape_id": "701", "nsets": 7, "type": "polygon" }
  ]
}
```
```

--------------------------------

### GET plot_shapes

Source: https://gaospecial.github.io/ggVennDiagram/reference/plot_shapes.html

Visualizes predefined Venn diagram shapes collected from internal datasets.

```APIDOC
## plot_shapes()

### Description
Plots all shapes provided by the internal dataset. These shapes are collected from the 'venn' and 'VennDiagram' packages to support Venn plots with more than 4 sets where simple circles or ellipses are insufficient.

### Details
- Shape 101, 201, 301, 401, 402, 501, 502, 601, and 701 are sourced from the 'venn' package.
- Shape 401f is sourced from the 'VennDiagram' package.

### Request Example
plot_shapes()
```

--------------------------------

### Construct and Plot Venn Diagram with Custom Shape

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-new-shapes.html

Demonstrates how to generate example data, construct a Venn object, process it with a specified shape ID ('402'), and then plot the resulting Venn diagram. This shows how to use specific internal shapes for custom plots.

```R
# Generate example data.
genes <- paste0("gene",1:1000)
set.seed(20210701)
gene_list <- list(A = sample(genes,100),
                  B = sample(genes,200),
                  C = sample(genes,300),
                  D = sample(genes,200))

# construct a Venn object
venn = Venn(gene_list)
data = process_data(venn, shape_id = "402")
plot_venn(data)
```

--------------------------------

### GET vensets()

Source: https://gaospecial.github.io/ggVennDiagram/reference/vensets.html

Retrieves a data frame containing the coordinates required to plot Venn diagram shapes.

```APIDOC
## GET vensets()

### Description
Imports and returns the coordinate data frame used for defining Venn diagram shapes.

### Method
GET

### Endpoint
vensets()

### Response
#### Success Response (200)
- **data frame** - A data frame containing the coordinate points for the Venn diagram shapes.
```

--------------------------------

### Get Venn Set Data

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Retrieves the data for each set within the Venn diagram. Useful for understanding the composition and counts of individual sets.

```R
venn_set(venn_plot_data)
#> # A tibble: 4 × 4
#>   id    name  item         count
#>   <chr> <chr> <named list> <int>
#> 1 1     A     <chr [8]>        8
#> 2 2     B     <chr [8]>        8
#> 3 3     C     <chr [8]>        8
#> 4 4     D     <chr [8]>        8
```

--------------------------------

### Get Applicable Shape Data

Source: https://gaospecial.github.io/ggVennDiagram/reference/get_shape_data.html

Retrieves data for shapes applicable to a Venn object based on the number of sets, shape type, and a specific shape ID.

```APIDOC
## GET /api/shapes/data

### Description
Retrieves data for shapes applicable to a Venn object. This function allows users to query internal shape data used by ggVennDiagram, specifying the number of sets, an optional shape type, and an optional shape ID.

### Method
GET

### Endpoint
/api/shapes/data

### Parameters
#### Query Parameters
- **nsets** (integer) - Required - The number of sets for which to retrieve shape data.
- **type** (string) - Optional - The type of shape to retrieve (e.g., "polygon").
- **shape_id** (string) - Optional - A specific ID for the shape to retrieve.

### Response
#### Success Response (200)
- **data** (tibble) - A tibble describing the specific shape, including its type, number of sets, number of regions, and methods to visualize it.

#### Response Example
```json
{
  "data": {
    "class": "VennPlotData",
    "id": "402",
    "type": "polygon",
    "nsets": 4,
    "nregions": 15,
    "description": "To view this shape, use `plot_shape_edge(get_shape_by_id('402'))`. To view its components, use `venn_setedge()`, `venn_setlabel()`, etc."
  }
}
```
```

--------------------------------

### Get Venn Region Edge Polygons

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Retrieves the coordinates for the edges of the regions (subsets) in the Venn diagram. This is useful for detailed visualization of the Venn diagram's geometry.

```R
venn_regionedge(venn_plot_data)
#> # A tibble: 713 × 6
#>    id        X     Y name  item      count
#>    <chr> <dbl> <dbl> <chr> <list>    <int>
#>  1 1     0.103 0.717 A     <chr [3]>     3
#>  2 1     0.112 0.726 A     <chr [3]>     3
#>  3 1     0.122 0.733 A     <chr [3]>     3
#>  4 1     0.133 0.740 A     <chr [3]>     3
#>  5 1     0.145 0.745 A     <chr [3]>     3
#>  6 1     0.158 0.749 A     <chr [3]>     3
#>  7 1     0.172 0.752 A     <chr [3]>     3
#>  8 1     0.186 0.754 A     <chr [3]>     3
#>  9 1     0.201 0.755 A     <chr [3]>     3
#> 10 1     0.217 0.755 A     <chr [3]>     3
#> # ℹ 703 more rows
```

--------------------------------

### Display Interactive Startup License Notice

Source: https://gaospecial.github.io/ggVennDiagram/LICENSE.html

Use this notice for programs that interact via terminal to inform users of the license and warranty status upon startup.

```text
ggVennDiagram Copyright (C) 2019 Chun-Hui Gao
This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type 'show c' for details.
```

--------------------------------

### Get Set Data from VennPlotData

Source: https://gaospecial.github.io/ggVennDiagram/articles/VennCalculator.html

Use `venn_set` to extract information about each individual set from the `VennPlotData` object.

```r
venn_set(pd)
#> # A tibble: 4 × 4
#>   id    name  item         count
#>   <chr> <chr> <named list> <int>
#> 1 1     A     <chr [8]>        8
#> 2 2     B     <chr [8]>        8
#> 3 3     C     <chr [8]>        8
#> 4 4     D     <chr [8]>        8
```

--------------------------------

### GET /get_shape_by_id

Source: https://gaospecial.github.io/ggVennDiagram/reference/get_shape_by_id.html

Retrieves a specific Venn diagram shape object based on the provided shape ID.

```APIDOC
## GET /get_shape_by_id

### Description
Retrieves a shape object associated with the specified unique identifier.

### Method
GET

### Endpoint
/get_shape_by_id

### Parameters
#### Query Parameters
- **id** (string) - Required - The unique identifier for the shape.

### Response
#### Success Response (200)
- **shape** (object) - The shape data object containing type, set count, and region information.

#### Response Example
{
  "id": "401f",
  "type": "ellipse",
  "sets": 4,
  "regions": 15
}
```

--------------------------------

### Venn Constructor and Show Method

Source: https://gaospecial.github.io/ggVennDiagram/reference/Venn-class.html

This snippet covers the constructor for the Venn class and the method to display Venn object information.

```APIDOC
## Venn Constructor and Show Method

### Description
This section describes how to create a Venn object and how to display its contents.

### Method
`Venn(sets, names = NULL)`

### Endpoint
N/A (R function)

### Parameters
#### Arguments
- **sets** (list) - Required - A list containing vectors in the same class. Duplicates will be discarded. If the list is unnamed, sets will be named 'Set_1', 'Set_2', etc.
- **names** (NULL or character vector) - Optional - The names of the sets.
- **object** (Venn) - Required - A Venn class object (used by the show method).

### Request Example
```R
venn_object <- Venn(sets = list(letters[1:10], letters[3:12], letters[6:15]), names = c("Set A", "Set B", "Set C"))
print(venn_object)
```

### Response
#### Success Response (Venn Object)
- **sets** (list) - A list object containing vectors in the same type.
- **names** (character vector) - The names of the sets.

#### Response Example
```
An object of class 'Venn':
   Slots: sets, names;
   No. Sets: 3   SetNames: Set A, Set B, Set C.
```
```

--------------------------------

### Configure Labels and Categories

Source: https://gaospecial.github.io/ggVennDiagram/index.html

Adjust category names and label visibility.

```R
ggVennDiagram(x,category.names = c("Stage 1","Stage 2","Stage 3", "Stage4"))
```

```R
ggVennDiagram(x,category.names = c("Stage 1","Stage 2","Stage 3", "Stage4"), label = "none")
```

```R
ggVennDiagram(x, label_alpha=0)
```

--------------------------------

### Launch Shiny App

Source: https://gaospecial.github.io/ggVennDiagram/reference/launch_app.html

Call this function to launch the Shiny app. The app returns a Shiny app object.

```R
launch_app()
```

--------------------------------

### Get Subset Data from VennPlotData

Source: https://gaospecial.github.io/ggVennDiagram/articles/VennCalculator.html

Use `venn_region` to extract data for each region (intersection/difference) within the Venn diagram from the `VennPlotData` object.

```r
venn_region(pd)
#> # A tibble: 15 × 4
#>    id      name    item      count
#>    <chr>   <chr>   <list>    <int>
#>  1 1       A       <chr [3]>     3
#>  2 2       B       <chr [4]>     4
#>  3 3       C       <chr [3]>     3
#>  4 4       D       <chr [3]>     3
#>  5 1/2     A/B     <chr [1]>     1
#>  6 1/3     A/C     <chr [2]>     2
#>  7 1/4     A/D     <chr [1]>     1
#>  8 2/3     B/C     <chr [0]>     0
#>  9 2/4     B/D     <chr [1]>     1
#> 10 3/4     C/D     <chr [1]>     1
#> 11 1/2/3   A/B/C   <chr [0]>     0
#> 12 1/2/4   A/B/D   <chr [0]>     0
#> 13 1/3/4   A/C/D   <chr [0]>     0
#> 14 2/3/4   B/C/D   <chr [1]>     1
#> 15 1/2/3/4 A/B/C/D <chr [1]>     1
```

--------------------------------

### Venn class methods

Source: https://gaospecial.github.io/ggVennDiagram/reference/Venn-class.html

Standard method signatures for creating a Venn object and displaying its contents.

```R
Venn(sets, names = NULL)

# S4 method for class 'ANY'
Venn(sets, names = NULL)

# S4 method for class 'Venn'
show(object)
```

--------------------------------

### Load required libraries for plotting

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Load ggVennDiagram and ggplot2 for manual plot construction.

```R
library(ggVennDiagram)
library(ggplot2)
```

--------------------------------

### Initialize Venn Data

Source: https://gaospecial.github.io/ggVennDiagram/articles/VennCalculator.html

Construct a Venn class object from a list of sets. Printing the object provides meta information.

```r
library(ggVennDiagram)
set.seed(20231225)
y = list(
  A = sample(letters, 8) |> sort(),
  B = sample(letters, 8) |> sort(),
  C = sample(letters, 8) |> sort(),
  D = sample(letters, 8) |> sort())

y
#> $A
#> [1] "a" "e" "g" "o" "p" "s" "t" "v"
#> 
#> $B
#> [1] "a" "d" "f" "i" "k" "s" "y" "z"
#> 
#> $C
#> [1] "b" "g" "k" "o" "r" "s" "u" "w"
#> 
#> $D
#> [1] "b" "c" "e" "h" "k" "q" "s" "y"
```

```r
venn_y = Venn(y)

venn_y
#> An object of class 'Venn':
#>    Slots: sets, names;
#>    No. Sets: 4   SetNames: A, B, C, D.
```

--------------------------------

### Get Venn Region Data

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Retrieves the data for each subset (region) of the Venn diagram, including intersections. This is essential for analyzing the overlap between sets.

```R
venn_region(venn_plot_data)
#> # A tibble: 15 × 4
#>    id      name    item      count
#>    <chr>   <chr>   <list>    <int>
#>  1 1       A       <chr [3]>     3
#>  2 2       B       <chr [4]>     4
#>  3 3       C       <chr [3]>     3
#>  4 4       D       <chr [3]>     3
#>  5 1/2     A/B     <chr [1]>     1
#>  6 1/3     A/C     <chr [2]>     2
#>  7 1/4     A/D     <chr [1]>     1
#>  8 2/3     B/C     <chr [0]>     0
#>  9 2/4     B/D     <chr [1]>     1
#> 10 3/4     C/D     <chr [1]>     1
#> 11 1/2/3   A/B/C   <chr [0]>     0
#> 12 1/2/4   A/B/D   <chr [0]>     0
#> 13 1/3/4   A/C/D   <chr [0]>     0
#> 14 2/3/4   B/C/D   <chr [1]>     1
#> 15 1/2/3/4 A/B/C/D <chr [1]>     1
```

--------------------------------

### Shiny Integration

Source: https://gaospecial.github.io/ggVennDiagram/reference/index.html

Utility to launch the interactive Shiny application.

```APIDOC
## launch_app()

### Description
Launches the Reactor Data Shiny App for interactive plotting.
```

--------------------------------

### Prepare Data for Venn Diagram

Source: https://gaospecial.github.io/ggVennDiagram/index.html

Create a list of sets to be used in the Venn diagram.

```R
library(ggVennDiagram)
genes <- paste("gene",1:1000,sep="")
set.seed(20231214)
x <- list(A=sample(genes,300),
          B=sample(genes,525),
          C=sample(genes,440),
          D=sample(genes,350))
```

--------------------------------

### Get Venn Set Edge Polygons

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Retrieves the coordinates for the edges of the sets in the Venn diagram. This data can be used for custom plotting or geometric analysis.

```R
venn_setedge(venn_plot_data)
#> # A tibble: 404 × 3
#>    id         X     Y
#>    <chr>  <dbl> <dbl>
#>  1 1     0.103  0.717
#>  2 1     0.0941 0.708
#>  3 1     0.0867 0.698
#>  4 1     0.0804 0.687
#>  5 1     0.0751 0.675
#>  6 1     0.0709 0.662
#>  7 1     0.0678 0.648
#>  8 1     0.0659 0.634
#>  9 1     0.0650 0.619
#> 10 1     0.0653 0.603
#> # ℹ 394 more rows
```

--------------------------------

### Initialize and display Venn object

Source: https://gaospecial.github.io/ggVennDiagram/reference/Venn-class.html

Constructs a new Venn object from a list of vectors and prints its summary information.

```R
venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
 print(venn)
```

--------------------------------

### Get Shape by ID

Source: https://gaospecial.github.io/ggVennDiagram/reference/get_shape_by_id.html

Use `get_shape_by_id` to retrieve a specific shape using its unique identifier. This function is useful for accessing pre-defined or previously saved shapes.

```R
get_shape_by_id("401f")
#> Class VennPlotData - '401f'
#>   Type: ellipse; No. sets: 4; No. regions: 15.
#>   To view this shape, use `plot_shape_edge(get_shape_by_id('401f'))`.
#>   To view its components, use `venn_setedge()`, `venn_setlabel()`, etc.
```

--------------------------------

### Calculate set differences

Source: https://gaospecial.github.io/ggVennDiagram/reference/discern.html

Demonstrates calculating the difference between sets using indices.

```R
venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
discern(venn, slice1 = 1)
#> [1] "a" "b"
discern(venn, slice1 = c(1, 2), slice2 = 3)
#> [1] "a" "b" "c" "d" "e"
```

--------------------------------

### VennPlotData Constructor

Source: https://gaospecial.github.io/ggVennDiagram/reference/VennPlotData.html

Initializes a VennPlotData object from a provided data source.

```APIDOC
## VennPlotData(x)

### Description
An S3 class constructor for representing Venn plot components.

### Arguments
- **x** (data source) - Required - The data source used to construct the VennPlotData object.

### Slots
- **shapeId** (string) - Identifier for the shape.
- **type** (string) - Type of the shape.
- **nsets** (integer) - Number of sets.
- **setEdge** (data.frame) - Coordinates of set edges.
- **setLabel** (data.frame) - Coordinates of set labels.
- **regionEdge** (data.frame) - Coordinates of different regions.
- **regionLabel** (data.frame) - Centroid of the regions where labels are anchored.
- **setData** (data.frame) - The set data provided by the user.
- **regionData** (data.frame) - The region data calculated by ggVennDiagram.
```

--------------------------------

### Get and Plot a Specific Shape by ID

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-new-shapes.html

Retrieves a specific shape using its ID and then plots its edges using ggplot2. This allows for detailed inspection and use of individual shapes.

```R
library(ggplot2)
shape2 = get_shape_by_id("401f")
plot_shape_edge(shape2)
```

--------------------------------

### Launch Reactor Data Shiny App

Source: https://gaospecial.github.io/ggVennDiagram/reference/launch_app.html

Launches the Reactor Data Shiny App. This function is part of the /websites/gaospecial_github_io_ggvenndiagram project.

```APIDOC
## Launch Reactor Data Shiny App

### Description
Launches the Reactor Data Shiny App.

### Method
N/A (Function Call)

### Endpoint
N/A (Function Call)

### Parameters
This function does not take any parameters.

### Request Example
```R
launch_app()
```

### Response
#### Success Response
- **app** (shiny app) - Returns the launched Shiny application.

#### Response Example
N/A (Launches an interactive app)
```

--------------------------------

### Create set list for analysis

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Generate a list of character vectors for set operations.

```R
set.seed(20231225)
y = list(
  A = sample(letters, 8) |> sort(),
  B = sample(letters, 8) |> sort(),
  C = sample(letters, 8) |> sort(),
  D = sample(letters, 8) |> sort())

# view the list
y
```

--------------------------------

### combinations(n)

Source: https://gaospecial.github.io/ggVennDiagram/reference/combinations.html

Calculates all possible combinations of n sets.

```APIDOC
## combinations(n)

### Description
Generates all possible combinations of n sets.

### Parameters
#### Arguments
- **n** (integer) - Required - The number of sets to calculate combinations for.
- **dim** (integer) - Optional - The dimension parameter.
```

--------------------------------

### Load ggVennDiagram Package

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-new-shapes.html

Loads the ggVennDiagram package for use in plotting Venn diagrams.

```R
library(ggVennDiagram)
```

--------------------------------

### Extract VennPlotData components

Source: https://gaospecial.github.io/ggVennDiagram/reference/venn_plot_data.html

Demonstrates how to process Venn data and extract various components using the provided accessor functions.

```R
venn = Venn(list(A=1:5,B=2:7,C=3:6,D=4:9))
obj = process_data(venn)
venn_regionlabel(obj)  # return regionLabel data
venn_regionedge(obj)   # return regionEdge data
venn_setlabel(obj) # return setLabel data
venn_setedge(obj)  # return setEdge data
venn_set(obj)     # set items
venn_region(obj)  # region items
```

--------------------------------

### Define Venn Object and Discern Overlap

Source: https://gaospecial.github.io/ggVennDiagram/reference/discern_overlap.html

Demonstrates creating a Venn object and using `discern_overlap` to find the total overlap. This is contrasted with the `overlap` function.

```R
library(ggVennDiagram)
venn <- Venn(list(A=1:3,B=2:5,C=c(1L,3L,5L)))

discern_overlap(venn, slice = "all")
#> [1] 3
# is equal to
overlap(venn, slice = "all")
#> [1] 3
```

--------------------------------

### Retrieve all available shapes

Source: https://gaospecial.github.io/ggVennDiagram/reference/get_shapes.html

Returns a tibble listing all supported shapes, their set capacity, and geometric classification.

```R
get_shapes()
```

```R
get_shapes()
#> # A tibble: 12 × 3
#>    shape_id nsets type    
#>    <chr>    <int> <chr>   
#>  1 101          1 circle  
#>  2 201f         2 circle  
#>  3 201          2 circle  
#>  4 301f         3 circle  
#>  5 301          3 circle  
#>  6 401f         4 ellipse 
#>  7 402          4 polygon 
#>  8 501          5 polygon 
#>  9 502          5 polygon 
#> 10 601t         6 triangle
#> 11 601          6 polygon 
#> 12 701          7 polygon
```

--------------------------------

### Construct Venn object

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Create a Venn object from a list.

```R
venn_y = Venn(y)

venn_y
```

--------------------------------

### Create Venn Object in R

Source: https://gaospecial.github.io/ggVennDiagram/reference/overlap.html

Initializes a Venn object with a list of sets. This is a prerequisite for performing set operations like overlap.

```r
venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
```

--------------------------------

### Check list element identity with all_identical

Source: https://gaospecial.github.io/ggVennDiagram/reference/all_identical.html

Use this function to verify if every member of a provided list is identical. It returns TRUE if all elements match, otherwise FALSE.

```R
all_identical(list)
```

--------------------------------

### Define unite method signature

Source: https://gaospecial.github.io/ggVennDiagram/reference/unite.html

Defines the S4 method signature for the unite function on a Venn object.

```R
unite(venn, slice = "all")

# S4 method for class 'Venn'
unite(venn, slice = "all")
```

--------------------------------

### unite(venn, slice)

Source: https://gaospecial.github.io/ggVennDiagram/reference/unite.html

Calculates the union of sets in a Venn object.

```APIDOC
## unite(venn, slice)

### Description
Returns the union of the sets in a Venn object.

### Parameters
#### Arguments
- **venn** (Venn object) - Required - A Venn object.
- **slice** (string/integer) - Optional - The names or the indices of sets of interest. Default is "all".

### Value
A vector showing the union of the sets.

### Request Example
venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
unite(venn, slice = c(1, 2))

### Response
- **result** (vector) - A vector containing the union of the specified sets.
```

--------------------------------

### Plotting multi-dimensional Venn diagrams

Source: https://gaospecial.github.io/ggVennDiagram/index.html

Demonstrates generating Venn diagrams for two to seven sets using a list of gene samples.

```R
x <- list(A=sample(genes,300),
          B=sample(genes,525),
          C=sample(genes,440),
          D=sample(genes,350),
          E=sample(genes,200),
          F=sample(genes,150),
          G=sample(genes,100))

# two dimension Venn plot
ggVennDiagram(x[1:2],label = "none")

# three dimension Venn plot
ggVennDiagram(x[1:3],label = "none")

# four dimension Venn plot
ggVennDiagram(x[1:4],label = "none")

# five dimension Venn plot
ggVennDiagram(x[1:5],label = "none")

# six dimension Venn plot
ggVennDiagram(x[1:6],label = "none")

# seven dimension Venn plot
ggVennDiagram(x,label = "none")
```

--------------------------------

### Plot All Available Internal Shapes

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-new-shapes.html

Generates plots for all internal shapes available in the package. This provides an overview of the different shapes and their structures.

```R
plot_shapes()
```

--------------------------------

### Automatic Upset plot generation

Source: https://gaospecial.github.io/ggVennDiagram/index.html

Shows how ggVennDiagram automatically switches to an Upset plot when the number of sets exceeds seven.

```R
# add an extra member in list
x$H = sample(genes,500)
ggVennDiagram(x)
#> Warning in ggVennDiagram(x): Only support 2-7 dimension Venn diagram. Will give a plain upset plot instead.
#> Warning: Removed 1 row containing missing values or values outside the scale range (`geom_col()`).
```

--------------------------------

### Perform set operations

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Calculate overlaps and differences between sets.

```R
# find the overlaping members of two or more sets
overlap(venn_y, 1:2) # members in both the first two sets
overlap(venn_y) # members in all the sets

# find the different members between sets and set unions
discern(venn_y, 1)  # members in set 1, but not in all the resting sets by default
discern(venn_y, c("A","B"), 3) # members in set A & B, but not in the third set

# find the specific members in one or more sets
discern_overlap(venn_y, 1)  # specific items in set 1, equals to `discern(venn_y, 1)`. Those members are not shared by all the other sets.
discern_overlap(venn_y, 1:2)  # specific items in set 1 and set 2
```

--------------------------------

### Add Plot Annotations

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-ggVennDiagram.html

Include titles, subtitles, and captions using ggplot2 labs.

```R
p + labs(title = "Fancy Venn Diagram of four sets",
         subtitle = "Generated by `ggVennDiagram`",
         caption = Sys.Date())
```

--------------------------------

### Customize Set Labels

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-ggVennDiagram.html

Adjust the color and size of the set labels.

```R
ggVennDiagram(gene_list, set_color = c("blue","black","red","yellow"))
```

```R
ggVennDiagram(gene_list, set_size = 8)
```

--------------------------------

### Define discern method signature

Source: https://gaospecial.github.io/ggVennDiagram/reference/discern.html

Defines the function signature for calculating set differences on a Venn object.

```R
discern(venn, slice1, slice2 = "all")

# S4 method for class 'Venn'
discern(venn, slice1, slice2 = "all")
```

--------------------------------

### Main Plotting Functions

Source: https://gaospecial.github.io/ggVennDiagram/reference/index.html

Core functions for generating Venn and Upset plots.

```APIDOC
## ggVennDiagram()

### Description
Main parser function for generating Venn diagrams.

## plot_venn()

### Description
Executes the plotting codes for a Venn diagram.

## plot_upset()

### Description
Generates an Upset plot from the provided data.
```

--------------------------------

### Access and View Internal Shape Data

Source: https://gaospecial.github.io/ggVennDiagram/articles/using-new-shapes.html

Demonstrates how to access a specific internal shape object and display its properties. The shape data is stored internally and can be inspected.

```R
shape1 = ggVennDiagram:::shapes[[4]]
shape1
```

--------------------------------

### Find Union of Sets

Source: https://gaospecial.github.io/ggVennDiagram/articles/VennCalculator.html

The `unite` function calculates the union of specified sets. It can take set indices, names, or 'all' for the union of all sets.

```r
unite(venn_y, 1:2) # union of set 1 and 2
#>  [1] "a" "e" "g" "o" "p" "s" "t" "v" "d" "f" "i" "k" "y" "z"
unite(venn_y, "all") # union of all four sets
#>  [1] "a" "e" "g" "o" "p" "s" "t" "v" "d" "f" "i" "k" "y" "z" "b" "r" "u" "w" "c"
#> [20] "h" "q"
unite(venn_y, c("A", "B", "C"))
#>  [1] "a" "e" "g" "o" "p" "s" "t" "v" "d" "f" "i" "k" "y" "z" "b" "r" "u" "w"
```

--------------------------------

### Reproduce ggVennDiagram plot manually

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Construct a Venn diagram using ggplot2 layers and processed Venn data.

```R
venn <- Venn(gene_list)
data <- process_data(venn)
ggplot() +
  # 1. region count layer
  geom_polygon(aes(X, Y, fill = count, group = id), 
          data = venn_regionedge(data)) +
  # 2. set edge layer
  geom_path(aes(X, Y, color = id, group = id), 
          data = venn_setedge(data), 
          show.legend = FALSE) +
  # 3. set label layer
  geom_text(aes(X, Y, label = name), 
               data = venn_setlabel(data)) +
  # 4. region label layer
  geom_label(aes(X, Y, label = count), 
                data = venn_regionlabel(data)) +
  coord_equal() +
  theme_void()
```

--------------------------------

### Plot Venn Diagram

Source: https://gaospecial.github.io/ggVennDiagram/reference/plot_venn.html

Use this function to generate Venn diagrams. Customize appearance with arguments like set_color, label, and edge_size. The show_intersect argument enables plotly visualization.

```R
plot_venn(
  data,
  show_intersect = FALSE,
  set_color = "black",
  set_size = NA,
  label = "both",
  label_geom = "label",
  label_alpha = 0.5,
  label_font = "sans",
  label_color = "black",
  label_size = NA,
  label_percent_digit = 0,
  label_bigMark = ",",
  label_bigInterval = 3L,
  label_txtWidth = 40,
  edge_lty = "solid",
  edge_size = 1,
  ...
)
```

--------------------------------

### Enable Interactive Intersections

Source: https://gaospecial.github.io/ggVennDiagram/index.html

Use the plotly method to view intersections interactively.

```R
ggVennDiagram(y, show_intersect = TRUE)
```

--------------------------------

### Print S3 Method for upsetPlotData

Source: https://gaospecial.github.io/ggVennDiagram/reference/print.html

This is the S3 print method for the upsetPlotData class. It is used to display the contents of an upsetPlotData object.

```R
# S3 method for class 'upsetPlotData'
print(x, ...)
```

--------------------------------

### Basic Upset Plot

Source: https://gaospecial.github.io/ggVennDiagram/reference/upset-plot.html

Generates a basic upset plot from a Venn object. Ensure the Venn object is created from a list of sets.

```R
 list = list(A = sample(LETTERS, 20),
             B = sample(LETTERS, 22),
             C = sample(LETTERS, 14),
             D = sample(LETTERS, 30, replace = TRUE))
 venn = Venn(list)
 plot_upset(venn)
```

--------------------------------

### all_identical Function

Source: https://gaospecial.github.io/ggVennDiagram/reference/all_identical.html

Checks if all members of a list have the same elements.

```APIDOC
## all_identical(list)

### Description
Checks if all members of a list have the same elements.

### Parameters
#### Arguments
- **list** (list) - Required - A list to be evaluated.

### Response
- **Value** (boolean) - Returns TRUE if all members are identical, otherwise FALSE.
```

--------------------------------

### Venn Plot Shapes Data

Source: https://gaospecial.github.io/ggVennDiagram/reference/shapes.html

This section describes the format and source of the shape data used to set up Venn plots. The data is a list containing several slots, as detailed in '?VennPlotData'. Sources include the 'venn' datasets by Adrian Dusa and parameters from 'VennDiagram' for advanced four-set ellipses.

```APIDOC
## Venn Plot Shapes Data

### Description
This describes the format of shape data used to set up Venn plots. This data defines the edge and label of sets within a Venn plot. You can view examples using `plot_shapes()`.

### Format
A list with several slots. Refer to `?VennPlotData` for more details.

### Source
- The `venn` datasets authored by Adrian Dusa (https://CRAN.R-project.org/package=venn).
- Parameters for generating four-set ellipses are adopted from `VennDiagram` (https://CRAN.R-project.org/package=VennDiagram).
- Wiki
```

--------------------------------

### Process plot data

Source: https://gaospecial.github.io/ggVennDiagram/articles/fully-customed

Convert a Venn object into plot-ready data.

```R
venn_plot_data = process_data(venn_y)
```

--------------------------------

### process_set_data

Source: https://gaospecial.github.io/ggVennDiagram/reference/venn_data.html

Extracts set-level data from a Venn object.

```APIDOC
## process_set_data

### Description
Processes a Venn object to return a tibble containing set information.

### Parameters
#### Arguments
- **venn** (Venn object) - Required - A Venn object.

### Response
- **Value** (tibble) - A tibble containing id, name, item, and count columns.
```
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