venn4Way: 4-way Venn Diagrams

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

4-way Venn Diagrams

Description

A function to create a 4-way Venn diagram

Usage

venn4Way(
  fit,
  contrast,
  p.value,
  lfc,
  adj.meth,
  baseUrl = ".",
  reportDirectory = "./venns",
  affy = TRUE,
  probecol = "PROBEID",
  ...
)

Arguments

fit	An MArrayLM object, created by the limma package.
contrast	A contrasts matrix, used by limma to generate the comparisons made.
p.value	A p-value cutoff for significance
lfc	A log fold change cutoff
adj.meth	The method used to adjust for multiple comparisons.
baseUrl	The base directory for the tables generated. Defaults to ".", meaning the current directory.
reportDirectory	The directory in which to put the results. Defaults to a "venns" subdirectory.
affy	Boolean. Set to TRUE if using Affymetrix microarrays.
probecol	The column containing either the Affymetrix probeset IDs (if the affy argument is set to TRUE) or the name of a column in the output tables that contains uinque identifiers (Entrez Gene IDs, gene symbols, etc).
...	Allows arbitrary arguments to be passed to lower level functions

Details

This function is an internal function and not really intended to be called by the end user. It is generally called by the vennPage function. The goal is to create a 4-way Venn diagram in an HTML page with clickable links to tables of the genes found in a given cell. In addition, the numbers in each cell are underlined with colored bars that help end users tell what contrasts are captured by that cell.

Value

Returns a list. The first item is a (list of) HTMLReportRef objects that can be used by ReportingTools to create HTML links. The second item is the output from the venn function in gtools, and the third item is the name of the contrasts used to generate the Venn diagram.

Author(s)

James W. MacDonald [e-mail]

jmacdon/affycoretools documentation built on Feb. 25, 2023, 4:51 a.m.