vennInLine: Generate Venn diagrams with links for Rmarkdown documents

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

Description

A function to generate Venn diagrams for use within Rmarkdown documents, particularly for those using the Bioconductor BiocStyle package for formatting.

Usage

vennInLine(
  vennlst,
  caplst,
  cex.venn = 1,
  shift.title = FALSE,
  reportDirectory = NULL,
  ...
)

Arguments

vennlst	The output from makeVenn.
caplst	A list of captions to accompany each Venn diagram.
cex.venn	Adjustment parameter for the numbers in the Venn diagram. The default is usually OK.
shift.title	Boolean. Should the titles for the Venn diagram be shifted to accommodate long contrast names?
reportDirectory	Directory containing the Venn diagram. This is usually set by makeVenn and for most people, the default NULL argument should be used.
...	Allows users to pass arbitrary arguments to lower level functions.

Details

This function is intended for those who use Rmarkdown documents to present results and who would like to include Venn diagrams showing the overlap between two to four contrasts. The Venn diagrams that are generated include links for each cell of the diagram that will open HTML pages that contain results for the genes that are found within the cell of the Venn diagram.

Please note that this function is tailored specifically for use within Rmarkdown documents, particularly those that use the Bioconductor BiocStyle package. The function call should be present in a code block using the argument results = "asis", because we are directly generating HTML rather than placing a figure.

Value

This function returns the required HTML text to generate the Venn diagram

Author(s)

James W. MacDonald [e-mail]

See Also

vennPage particularly for the example.

affycoretools documentation built on Nov. 8, 2020, 6 p.m.