# Tutorial: Using ggVennDiagram

‘`ggVennDiagram`’ enables fancy Venn plot with 2-7 sets and generates publication quality figure.

## Installation

You can install the released version of ggVennDiagram from CRAN with:

    install.packages("ggVennDiagram")

And the development version from GitHub with:

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

## Usage

Generate example data.

    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)

## long category names

If you use long category names in Venn plot, labels may be cropped by plot borders. To avoid this, just use a ggplot trick to expand x axis.

    p1 <- ggVennDiagram(gene_list,
                        category.names = c("a very long name","short name","name","another name"))
    p1

    # expand axis to show long set labels
    p1 + scale_x_continuous(expand = expansion(mult = .2))

## Show intersection values

When intersection values only have several members, `ggVennDiagram` is efficient to show the values in places.

    set.seed(0)
    small_list <- lapply(sample(6:10, size = 4), function(x){
      sample(letters,x)
    })

    ggVennDiagram(small_list,
                        category.names = LETTERS[1:4],
                        show_intersect = TRUE)
    #> Warning in geom_text(aes_string(label = "count", text = "text"), x =
    #> label_coord[, : Ignoring unknown aesthetics: text

## Setting set label

### color of set label

    ggVennDiagram(gene_list, set_color = c("blue","black","red","green"))

### size of set labels

    ggVennDiagram(gene_list, set_size = 8)

## Setting region label

### text content

    ggVennDiagram(gene_list, label = "count")

    ggVennDiagram(gene_list, label = "percent")

### percentage digits

    ggVennDiagram(gene_list, label_percent_digit = 1, label = "percent")

### remove label background

- Method 1: set alpha to 0

    ggVennDiagram(gene_list, label_alpha = 0)

- Method 2: use `geom_text()`

    ggVennDiagram(gene_list, label_geom = "text")

### color and size

    ggVennDiagram(gene_list, label_color = "firebrick", label_size = 4)

## Setting set edges

    ggVennDiagram(gene_list, edge_lty = "dashed", edge_size = 1)

## Changing palette

- changing fill palette

    library(ggplot2)
    p <- ggVennDiagram(gene_list)

    # Red Blue
    p + scale_fill_distiller(palette = "RdBu")

    # Reds
    p + scale_fill_distiller(palette = "Reds", direction = 1)

- change edge colors

    p + scale_color_brewer(palette = "Set1")

Some other palletes are:

    RColorBrewer::display.brewer.all()

## Adding note

    p + labs(title = "Four sets Venn Diagram",
             subtitle = "generated by `ggVennDiagram`",
             caption = Sys.Date())