## ----install,eval = FALSE----------------------------------------------------- # if (!requireNamespace("BiocManager")) # install.packages("BiocManager") # `BiocManager::install("VennDetail") ## ----load, results = 'hide', message = FALSE---------------------------------- library(VennDetail) data(T2DM) ## ----quick-------------------------------------------------------------------- ven <- venndetail(list(Cortex = T2DM$Cortex$Entrez, SCN = T2DM$SCN$Entrez, Glom = T2DM$Glom$Entrez)) ## ----fig1, fig.width = 6, fig.height = 5, fig.align = "center"---------------- ##traditional venn diagram plot(ven) ## ----fig2, fig.width = 6, fig.height = 5, fig.align = "center"---------------- ##Venn-Pie format plot(ven, type = "vennpie") ## ----fig3, fig.width = 6, fig.height = 5, fig.align = "center"---------------- ##Upset format plot(ven, type = "upset") ## ----get---------------------------------------------------------------------- ## List the subsets name detail(ven) head(getSet(ven, subset = c("Shared", "SCN")), 10) ## ----result------------------------------------------------------------------- ## long format: the first column lists the subsets name, and the second column ## shows the genes included in the subsets head(result(ven)) ## wide format: the first column lists all the genes, the following columns ## display the groups name (three tissues) and the last column is the total ## number of the gene shared by groups. head(result(ven, wide = TRUE)) ## ----fig4, fig.width = 6, fig.height = 5, fig.align = "center"---------------- vennpie(ven, any = 1, revcolor = "lightgrey") ## ----fig5, fig.width = 6, fig.height = 5, fig.align = "center"---------------- vennpie(ven, log = TRUE) ## ----fig6, fig.width = 6, fig.height = 5, fig.align = "center"---------------- set.seed(123) A <- sample(1:1000, 400, replace = FALSE) B <- sample(1:1000, 600, replace = FALSE) C <- sample(1:1000, 350, replace = FALSE) D <- sample(1:1000, 550, replace = FALSE) E <- sample(1:1000, 450, replace = FALSE) venn <- venndetail(list(A = A, B = B, C= C, D = D, E = E)) vennpie(venn, min = 4) ## ----getfeature--------------------------------------------------------------- head(getFeature(ven, subset = "Shared", rlist = T2DM)) ## ----fig7, fig.width = 6, fig.height = 5, fig.align = "center"---------------- dplot(ven, order = TRUE, textsize = 4)