Nothing
knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 7, fig.asp = 0.618, fig.align = "center" )
'ggVennDiagram
' enables fancy Venn plot with 2-7 sets and generates publication quality figure.
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")
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)
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))
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)
ggVennDiagram(gene_list, set_color = c("blue","black","red","yellow"))
ggVennDiagram(gene_list, set_size = 8)
ggVennDiagram(gene_list, label = "count") ggVennDiagram(gene_list, label = "percent") ggVennDiagram(gene_list, label = "both") ggVennDiagram(gene_list, label = "none")
plots = lapply(c("none","count","percent","both"), function(x){ ggVennDiagram(gene_list,label = x) + labs(title = paste0('label = "', x, '"')) + theme(legend.position = "none") }) aplot::plot_list(gglist = plots, ncol = 2, labels = LETTERS[1:4])
ggVennDiagram(gene_list, label_percent_digit = 1, label = "percent")
ggVennDiagram(gene_list, label_alpha = 0)
geom_text()
ggVennDiagram(gene_list, label_geom = "text")
ggVennDiagram(gene_list, label_color = "firebrick", label_size = 4)
ggVennDiagram(gene_list, edge_lty = "dashed", edge_size = 1)
library(ggplot2) p <- ggVennDiagram(gene_list) # Red Blue p + scale_fill_distiller(palette = "RdBu") # Reds p + scale_fill_distiller(palette = "Reds", direction = 1)
Some other palletes are:
RColorBrewer::display.brewer.all()
p + labs(title = "Fancy Venn Diagram of four sets", subtitle = "Generated by `ggVennDiagram`", caption = Sys.Date())
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