venndia: venndia

In bakuhatsu/microarrayTools: Tools for microarray data analysis

venndia

Description

venndia takes two objects (A and B) each with up- and down-regulated genelists. To make a list containing two lists: 1) up-regulated genes, and 2) down-regulated genes. venndia is currently case-sensitive, so please provide list in all capitals.

Usage

venndia(A, B, titleA = "", titleB = "", getdata = FALSE,
  getcounts = FALSE, border = NA, NoAandB = FALSE, highLow = "redGreen",
  noPlot = FALSE, font = 1, backgrd = c(1, 2), ...)

Arguments

A	A geneset object, which is a list containing two vectors $UP and $DN which are lists of up-regulated and downregulated genes in a comparison.
B	Another geneset object for identifying overlap with geneset A.
titleA	A title for the left circle (dataset A)
titleB	A title for the right cirlce (dataset B)
getdata	Set to TRUE to return a geneset object for A-only, AB-overlap, and B-only. (Use $A, $AB, or $B after the function call to specify which and you can feed this into another venndia call)
getcounts	Set to TRUE to return a list the number of genes up- or down-regulated for A-only, AB-overlap, and B-only. Use $A, $AB, or $B after the function call to specify which if desired. getdata overrides getcounts (you can't do both)
border	Set "black" to add a black border around circles.
NoAandB	Set TRUE to remove the "A" and "B" from the plot.
highLow	Choose the font color scheme for numbers of up- and down-regulate genes: redGreen or pinkBlue
noPlot	Set FALSE to prevent plot from displaying (useful when getdata is set to TRUE and geneset is passed to another venndia call).
font	Select font size (default is 1).
backgrd	Select the background colors for circles by passing a vector of length 2 containing two integers from 1 to 12. Recommended: default = c(1,2), c(3,4), c(5,6), c(7,8), c(9,10), c(11,12).
...	Possible other parameters.

Value

A Venn diagram visualization and/or a geneset object containg lists of up- and down-regulated genes.

Examples

## For the two genesets to compare:
#' # Example data is provided, use the following code to load it
data("GeneSetdata") # loads GeneSet_UP and GeneSet_DOWN objects which contain example data.

## Make a list containing two vectors: 1) up-regulated genes, and 2) down-regulated gene
## Create geneset A
GeneSetA <- list()
GeneSetA$UP <- GeneSet_UP[sample(1:200, 100)] # Random set of 100 genes up
GeneSetA$DN <- GeneSet_DOWN[sample(1:200, 100)] # Random set of 100 genes down

GeneSetB <- list()
GeneSetB$UP <- GeneSet_UP[sample(1:200, 100)] # Random set of 100 genes up
GeneSetB$DN <- GeneSet_DOWN[sample(1:200, 100)] # Random set of 100 genes down

## Test the overlap
venndia(GeneSetA, GeneSetB) # Outputs a graphic

## Get the results of the overlap between A and B
venndia(GeneSetA,GeneSetB, getdata = TRUE)$AB

## Compare this overlap with a third geneset (GeneSetC).
GeneSetC <- list()
GeneSetC$UP <- GeneSet_UP[sample(1:200, 100)] # Random set of 100 genes up
GeneSetC$DN <- GeneSet_DOWN[sample(1:200, 100)] # Random set of 100 genes down

overlapAB <- venndia(GeneSetA,GeneSetB, getdata = TRUE)$AB

venndia(overlapAB, GeneSetC)

## Prettier version
venndia(overlapAB, GeneSetC, NoAandB = TRUE, border = "black")

bakuhatsu/microarrayTools documentation built on March 26, 2024, 8:53 p.m.