vennPage: High-level function for making Venn diagrams with clickable...

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

Description

This function is designed to be used in conjunction with the makeVenn function, to first create a set of HTML pages containing the genes that are represented by the cells of a Venn diagram, and then create an HTML page with the same Venn diagrams, with clickable links that will point the end user to the HTML pages.

Usage

vennPage(
  vennlst,
  pagename,
  pagetitle,
  cex.venn = 1,
  shift.title = FALSE,
  baseUrl = ".",
  reportDirectory = NULL,
  ...
)

Arguments

vennlst	The output from makeVenn.
pagename	Character. The file name for the resulting HTML page. Something like 'venns' is reasonable. Note that the .html will automatically be appended.
pagetitle	Character. The heading for the HTML page.
cex.venn	Numeric. Adjusts the size of the font in the Venn diagram. Usually the default is OK.
shift.title	Boolean. Should the right contrast name of the Venn diagram be shifted down? Useful for long contrast names. If a two-way Venn diagram, this will shift the right name down so they don't overlap. If a three-way Venn diagram, this will shift the top right name down.
baseUrl	Character. The base URL for the resulting HTML page. The default of "." is usually optimal.
reportDirectory	If NULL, the reportDirectory will be extracted from the vennlst. This is usually what one should do.
...	To allow passing other arguments to lower level functions. Currently not used.

Details

This function is intended to be used as part of a pipeline, by first calling makeVenn and then using the output from that function as input to this function to create the HTML page with clickable links.

Value

An HTMLReport object. If used as input to the ReportingTools publish function, this will create a link on an index page to the Venn diagram HTML page. See e.g., the microarray analysis vignette for ReportingTools for more information.

Author(s)

James W. MacDonald [e-mail]

Examples

  ## Not run: 
    mat <- matrix(rnorm(1e6), ncol = 20)
    design <- model.matrix(~factor(1:4, each=5))
    colnames(design) <- LETTERS[1:4]
    contrast <- matrix(c(1,-1,0,0,1,0,-1,0,1,0,0,-1,0,1,-1,0,0,1,0,-1),
    ncol = 5)
    colnames(contrast) <- paste(LETTERS[c(1,1,1,2,2)],
    LETTERS[c(2,3,4,3,4)], sep = " vs ")
    fit <- lmFit(mat, design)
    fit2 <- contrasts.fit(fit, contrast)
    fit2 <- eBayes(fit2)
    ## two Venn diagrams - a 3-way Venn with the first three contrasts
    ## and a 2-way Venn with the last two contrasts
    collist <- list(1:3,4:5)
    venn <- makeVenn(fit2, contrast, design, eset, collist = collist)
    vennreport <- vennPage(venn, "index.html", "Venn diagrams")
    indexPage <- HTMLReport("index", "My results", reportDirectory =
    ".", baseUrl = ".")
    publish(vennreport)
    finish(indexPage)
    
## End(Not run)

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