using-new-shapes.Rmd

---
title: "Using New Shapes in Venn Diagram"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Using New Shapes in Venn Diagram}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```


```{r setup}
library(ggVennDiagram)
```

## Internal Shapes

The **ggVennDiagram** package has a set of built-in shapes that are used to plot
Venn diagram. These internal data are stored as sys data as a tibble. It can be
accessed with `ggVennDiagram:::shapes` and viewed by the function `get_shapes()`, 
and plotted with the function `plot_shapes()`.

```{r}
shape1 = ggVennDiagram:::shapes[[4]]
shape1
```
The format of these shapes data are defined in `VennPlotData` class. Use `?VennPlotData` to view the document.

```{r}
plot_shape_edge(shape1)
```

`get_shapes()` will extract the meta features of these shapes and output a tibble. These information can be used for sepecifying a shape either by its id, or type.

```{r}
get_shapes()
```

For example, if you want to extract the shape whose id is "401f". This time we use `ggplot2` functions to plot the set edge of it.

```{r}
library(ggplot2)
shape2 = get_shape_by_id("401f")
plot_shape_edge(shape2)
```

The `plot_shapes()` function can be used to plot all the available shapes stored in this package. Please note that the shapes for this five sets diagram, as well as those for six and seven sets, are imported from the original package [`venn`](https://CRAN.R-project.org/package=venn), authored by Adrian Dușa.


```{r}
plot_shapes()
```

Among them, the shapes with less than four sets can be generated with circle or ellipses. For example, the parameters used to generate four-set ellipses were adopted from `VennDiagram` (<https://CRAN.R-project.org/package=VennDiagram>). Notably, those shapes of five or more sets, including 501, 502, 601, and 701, are created by Adrian Dușa and provided in his `venn` package (<https://CRAN.R-project.org/package=venn>). Besides, the 601t shape is imported from a WiKi entry (<https://en.wikipedia.org/wiki/Venn_diagram>).


## Using alternative internal shapes

By default, only the most appropriate shape is used when calling the main function
`ggVennDiagram()`. However, it may be specified in step wise plot which has been
described in [fully customed plot](https://gaospecial.github.io/ggVennDiagram/articles/fully-customed).

For example:


```{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)
```

## Using a novel shape

If user knows the coordinates of a novel shape, it may also be used to draw in 
`ggVennDiagram`. The functions of this part have been transfered to a new R package 
`shapeMageR`, which can be found in <https://github.com/gaospecial/shapeMageR>.
To do this, the dependency of `ggVennDiagram` is very light, thus increase the 
accessibility of the package.


## Reference

Adrian Dușa (2024) _venn: Draw Venn Diagrams_, R package version 1.12. <https://CRAN.R-project.org/package=venn>.