Skip to content

VennDetail: a bioconductor package for VennDiagram visualization and details extraction

Notifications You must be signed in to change notification settings

guokai8/VennDetail

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

VennDetail

Project Status: Active - The project has reached a stable, usable state and is being actively developed. Bioc platform BuildStatus

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]

About

VennDetail: a bioconductor package for VennDiagram visualization and details extraction

Topics

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages