mouseOverHtmlFile: Create mouse-over interactive html-pages (with links)

Description

This function allows generating html pages with interactive mouse-over to display information for the points of the plot and www-links when clicking based on embedded png file. Basically, an html page will be generated which contains a call to display to an image file specified in pngFileNa and in the body below pixel-coordinated will be given for disply of information at mouse-over and embedded links.

Usage

mouseOverHtmlFile(
  myCoor,
  pngFileNa,
  HtmFileNa = NULL,
  mouseOverTxt = NULL,
  displSi = c(800, 600),
  colNa = NULL,
  tit = "",
  myHtmTit = "",
  myComment = NULL,
  textAtStart = NULL,
  textAtEnd = NULL,
  pxDiam = 5,
  addLinks = NULL,
  linkExt = NULL,
  htmlExt = "htm",
  callFrom = NULL,
  silent = FALSE
)

Arguments

myCoor

(matrix or data.frame) with initial x&y coordinates of points for plot; with IDs (1st column !!) & coordinates (2nd & 3rd col), data for mouse-over & link (4th & 5th); NOTE : if 'colNa' NOT given, colnames of 'myCoor' will be inspected & filtered (columns of non-conform names may get lost) !!! Associated with (already existing) figure file 'pngFileNa' and make html page where points may be indicated by mouse-over

pngFileNa

(character, length=1) filename for complementary png figure (must already exist)

HtmFileNa

(character, length=1) filename for html file produced

mouseOverTxt

(character, length=1) text for interactive mouse-over in html, if NULL, will use col specified by 1st 'colNa' or (if NULL) rownames of 'myCoor'

displSi

(integer, length=2) size of image ('pngFileNa') at display in html (width,height), see also par

colNa

(character) if not NULL min length of 3 to custom specify the column-names to be used : 1st for mouse-over and 2nd+3rd for coordinates associated (and optional 4th for links)

tit

(character) title to be displayed on top of figure

myHtmTit

(character) title of Html page; 'htmlExt' .. checking and correcting filename-extension (only main Html page)

myComment

(character) modify comment embedded in html-document

textAtStart

(character) text in html before figure

textAtEnd

(character) text in html after figure

pxDiam

(integer, length=1) diameter for mouse-over tip to appear (single val or vector), simpler version/solution than with 'Tooltip' package

addLinks

(character) for clickable links, either 1) vector of links or 2) single character-chain to be used for pasting to rownames (eg https://www.uniprot.org/uniprot/) or 3) TRUE to check presence of 4th name specified in 'colNa' to be useed as columname from 'myCoor' dominates over eventual presence of 4th name in 'colNa'

linkExt

(character) if specified : links will get specified ending, define as NULL or "" for taking 'addLinks' asIs

htmlExt

(character, length=1) extension used when making html files

callFrom

(character) allow easier tracking of message(s) produced

silent

(logical) suppress messages

Value

plot

Details

Basically theer are two options for defining the path to the image embedded : 1) Absolute path : I turn you can moove the html to different locations, as long as it still can see the png-file the image can be displayed. However, this may not be any more the case when the html file is sent to another person. If the png-file is accessible as url, it should be easily visible. 2) Relative path : The simplest case would be to give only the file-name with no path at all, thus the png-file is supposed to be in the same directory as the html-file. This option is very 'transportable'. Basically the same applies to the clickable links which may be provided. In high-throughput biology one typically points here to data-bases accessible over the internet where urls to specific pages. With UniProt such links can easily be constructed when using protein identifiers as rownames.

Examples

Run this code

# NOT RUN {
## Note, this example writes files to R's tempdir,
## Otherwise, if you simply work in the current directory without spcifying paths you'll 
##  get an html with relatove paths, which simply needs the png file in the same path 
df1 <- data.frame(id=letters[1:10],x=1:10,y=rep(5,10),mou=paste("point",letters[1:10]),
  link=file.path(tempdir(),paste(LETTERS[1:10],".html",sep="")),stringsAsFactors=FALSE)  
## here we'll use R's tempdir, later you may want to choose other locations
pngFile <- file.path(tempdir(),"test01.png")
png(pngFile,width=800, height=600,res=72)
## here we'll just plot a set of horiontal points ...
plot(df1[,2:3],las=1,main="test01")
dev.off()
## Note : Special characters should be converted for display in html pages during mouse-over
library(wrMisc)
df1$mou <- htmlSpecCharConv(df1$mou)
## Let's add the x- and y-coordiates of the points in pixels to the data.frame
df1 <- cbind(df1,convertPlotCoordPix(x=df1[,2],y=df1[,3],plotD=c(800,600),plotRes=72))
head(df1)
## Now make the html-page allowing to display mouse-over to the png made before
htmFile <- file.path(tempdir(),"test01.html")
mouseOverHtmlFile(df1,pngFile,HtmFileNa=htmFile,pxDiam=15,
  textAtStart="Points in the figure are interactive to mouse-over ...",
  textAtEnd="and/or may contain links")
## We still need to make some toy links
for(i in 1:nrow(df1)) cat(paste("point no ",i," : ",df1[i,1]," x=",df1[i,2]," y=",
  df1[i,3],sep=""), file=df1$link[i]) 
## Now we are ready to open the html file using any browser
# }
# NOT RUN {
browseURL(htmFile)
# }