createVennEuler: A createVennEuler Function

In uebvhir/uebVennDiagram: Venn and Euler diagrams from lists of elements (top tables), creating the corresponding table of shared and non-shared elements

Description

Generates Venn and Euler diagram from lists of elements (top tables) with the corresponding lists of shared and non-shared elements

Usage

createVennEuler(topTabs, compNames, label = "selected", colFeat = "X",
  colPVal = "P.Value", pval = 0.05, pltR = TRUE, pltPdf = TRUE,
  venn = TRUE, eul = TRUE, csv = TRUE)

Arguments

topTabs	= list of data frames (which are expected to be in "topTable" shape) to be used as input data
compNames	= labels (character vector), corresponding with each input list, to be used in the plots and output table
label	= name (character) to be included as global label in all output files created
colFeat	= name (character) of the column where to look for the elements to be compared (such as "Name", "Symbol" or "GeneID")
colPVal	= name (character) of the column with p-values to be used as filtering criteria, such as "Adj.p.val" or "P.value"
pval	= threshold (numeric) value to be applied for filtering by p-value (0.05 means to filter out cases with p-val>0.05)
pltR	= TRUE/FALSE, to determine if the plots should be done directly in R
pltPdf	= TRUE/FALSE, to determine if the plots should be done in an output PDF file
venn	= TRUE/FALSE, to determine whether or not to plot the Venn diagram
eul	= TRUE/FALSE, to determine whether or not to plot the Euler diagram
csv=	TRUE/FALSE, to determine whether or not to write the table of shared elements as csv output file

Value

sharedElements (data.frame): table with elements shared by each combination of lists provided

Author(s)

Miriam Mota <[e-mail]> and Ferran Brianso <[e-mail]>

References

Hanbo Chen (2014). VennDiagram: Generate high-resolution Venn and Euler plots. R package version 1.6.9. https://CRAN.R-project.org/package=VennDiagram

Lee Wilkinson (2011). venneuler: Venn and Euler Diagrams. R package version 1.1-0. https://CRAN.R-project.org/package=venneuler

Examples

## load("topTableList.RData") # this loads the topTableList data object
## load("compNamesList.RData") # this loads the topTableList data object
## compNamesList <- c("A1vsB1","A1vsC1","B1vsC1","A2vsB2","A2vsC2")
sharedElems <- createVennEuler(topTabs = topTableList,
                               compNames = compNamesList,
                               label = "demo",
                               colFeat = "Name",
                               colPVal = "P.Value",
                               pval = 0.01,
                               pltR = TRUE,
                               pltPdf = TRUE,
                               eul = TRUE,
                               venn = TRUE,
                               csv = TRUE)

uebvhir/uebVennDiagram documentation built on May 3, 2019, 2:22 p.m.