View source: R/reportingTools.R
vennPage | R Documentation |
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.
vennPage( vennlst, pagename, pagetitle, cex.venn = 1, shift.title = FALSE, baseUrl = ".", reportDirectory = NULL, ... )
vennlst |
The output from |
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 |
... |
To allow passing other arguments to lower level functions. Currently not used. |
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.
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.
James W. MacDonald jmacdon@u.washington.edu
## 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.