VennDetail
VennDetail An R package for visualizing and extracting details of multi-sets
intersection
Description
Visualizing and extracting unique (disjoint) or overlapping subsets of multiple gene datasets are a frequently performed task for bioinformatics. Although various packages and web applications are available, no R package offering functions to extract and combine details of these subsets with user datasets in data frame is available. Moreover, graphical visualization is usually limited to six or less gene datasets and a novel method is required to properly show the subset details. We have developed VennDetail, an R package to generate high-quality Venn-Pie charts and to allow extraction of subset details from input datasets.
Installation
library(devtools)
install_github("guokai8/VennDetail")
##Or install from Bioconductor
BiocManager::install("VennDetail")
Getting started
library(VennDetail)
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)
res <- venndetail(list(A = A, B = B, C = C, D = D))
result <- result(res)
head(result)
Software Usage
getSet(res, "A") # get unique elements in A
summary(res) #show overlap 'details' of all subsets
dplot(res) #make a bargraph for 'details'
dA <- data.frame(A = A, "FC" = rnorm(400))
dB <- data.frame(B = B, "FC" = rnorm(600))
dC <- data.frame(C = C, "FC" = rnorm(350))
dD <- data.frame(D = D, "FC" = rnorm(550))
getFeature(res, subset = "Shared", rlist = list(dA, dB, dC, dD),
userowname = FALSE, gind = c("A", "B", "C", "D"))
###As all these four dataframes don't have row names, we set userowname to be FALSE
Shiny web app
VennDetail Note: Only support five input datasets now
Contact information
For any questions please contact [email protected]