R/annotateSvg.R

In arrayQualityMetrics: Quality metrics report for microarray data sets

## --------------------------------------------------------------------------------------------------------
## Postprocess an SVG file:
##  1. add an 'id' attribute to the root svg element
##  2. add mouse events to the elements of interest (found by the function annotationInfo@getPlotObjNodes)
##  3. the ids of the symbols that are defined in the <defs> elements are -by libcairo- of the form
##     glyph0-0, glyph1-0 etc. Since we are going to inline the content from all svg files into a single html
##     document, these id would clash between different svg plots, and need to by made unique. I wonder
##     whether a more elegant way exists for this.
## ---------------------------------------------------------------------------------------------------------
# annotateSvgPlot = function(infile, outfile, outdir, annotationInfo, name)
#   {
# 
#     ## Check argument
#     stopifnot(is(annotationInfo, "svgParameters"))
# 
#     doc = xmlParse(infile)
#     vb  = getViewBox(doc)
# 
#     svg = xmlRoot(doc)
# 
#     ## 1. add id
#     xmlAttrs(svg) = c(id = paste("Fig", name, sep=":"))
# 
#     ## monitor our success in finding what we expect
#     isok = c(symbol = FALSE, clipPath = FALSE, use = FALSE, cp = FALSE, plotobjs = FALSE)
# 
#     ## 2. this part is brittle - 'getPlotObjNodes' will be 'getMatplotSeries' or 'getPlotPoints' from
#     ## 'SVGAnnotation', which rely on conventions used by libcairo to produce the SVG
#     ## from the R plot, on simple pattern matching and on hope that the found patterns
#     ## align with the intended plot objects (i.e. not on any explicit identification).
#     plotobjs = try(annotationInfo@getPlotObjNodes(doc))
# 
#     if( (!is(plotobjs, "try-error")) && (length(plotobjs) == annotationInfo@numPlotObjects) )
#       {
#          succeeded = 0
#          for(i in seq_along(plotobjs))
#           {
#             roid = annotationInfo@getReportObjIdFromPlotObjId(i)
#             stopifnot(length(roid)==1, is.integer(roid))
#             callbacks = sprintf("plotObjRespond('%s', %d, '%s')", c("click", "show", "hide"), roid, name)
# 
#             if(!is(try({
#                 xmlAttrs(plotobjs[[i]]) = c(
#                       "class"       = paste0("aqm", roid),
#                       "onclick"     = callbacks[1],
#                       "onmouseover" = callbacks[2],
#                       "onmouseout"  = callbacks[3])
#                 convertCSSStylesToSVG(plotobjs[[i]])
#             }), "try-error"))
#                 succeeded = succeeded + 1
#           } ## for
#           if (succeeded == length(plotobjs))
#               isok["plotobjs"] = TRUE
#       }
# 
#     ## 3. find the children of the <defs> element that are <symbol>, and also <clipPath>
#     isok["symbol"]   = renameNodes(doc, "//x:defs/x:g/x:symbol", prefix = name)
#     isok["clipPath"] = renameNodes(doc, "//x:clipPath", prefix = name)
# 
#     ## similarly, find the <use> elements ...
#     use = getNodeSet(doc, "//x:use", "x")
#     if(length(use)>0)
#       {
#         oldvalues = sapply(use, function(x) xmlAttrs(x)["href"])
#         stopifnot(all(grepl("^#", oldvalues)))
#         newvalues = sub("#", paste0("#", name, "-"), oldvalues)
#         names(newvalues) = rep("xlink:href", length(newvalues))
#         for(i in seq_along(use))
#           xmlAttrs(use[[i]]) = newvalues[i]
#         isok["use"] = TRUE
#       }
# 
#     ## ... and the <g> elements that use a clip-path attribute
#     cp = getNodeSet(doc, "//x:g[@clip-path]", "x")
#     if(length(cp)>0)
#       {
#         oldvalues = sapply(cp, function(x) xmlAttrs(x)["clip-path"])
#         stopifnot(all(grepl("^url\\(#", oldvalues)))
#         newvalues = sub("#", paste0("#", name, "-"), oldvalues)
#         for(i in seq_along(cp))
#           xmlAttrs(cp[[i]]) = newvalues[i]
#         isok["cp"] = TRUE
#       }
# 
#     #saveXML(doc, file.path(outdir, outfile))
#     writeLines(saveXML(doc), file.path(outdir, outfile)) # get SVG with line breaks
# 
#     return(list(size = diff(vb), annotateOK = all(isok[c("symbol", "use", "plotobjs")]))) # clip-path related annotations are not vital
#   }
# 
# 
# annotateSvgGrid = function(annotationInfo, name) {
#   ## Check argument
#   stopifnot(is(annotationInfo, "svgParameters"))
#   
#   numPlotObjects = annotationInfo@numPlotObjects
#   roid = annotationInfo@getReportObjIdFromPlotObjId(seq_len(numPlotObjects))
#   isok = FALSE
#   
#   class     = paste0("aqm", roid)
#   callbacks = matrix(sprintf("plotObjRespond('%s', %d, '%s')", c("click", "show", "hide"), rep(roid, each=3), name), nrow=numPlotObjects, ncol=3, byrow=TRUE)
#     
#   if(annotationInfo@gridObjId == "xyplot.lines"){
#     # Iterate through line groups
#     # Note: the code below is based on the assumption that the number of report objects equals
#     # length(unique(roid)) and objects with same id are distributed among different panels
#     
#     numReportObjects = length(unique(roid))
#     numPanels = numPlotObjects %/% numReportObjects
#     panelIndices = seq.int(0L, by = numReportObjects, length.out = numPanels)
#     
#     for(i in seq_len(numReportObjects))
#       grid.garnish(paste(annotationInfo@gridObjId, "group", sep=".", i), group=FALSE, grep=TRUE, global=TRUE,
#                    class       = class[panelIndices+i],
#                    onclick     = callbacks[panelIndices+i, 1],
#                    onmouseover = callbacks[panelIndices+i, 2],
#                    onmouseout  = callbacks[panelIndices+i, 3])
#     isok = TRUE
#   }
#   else if(annotationInfo@gridObjId == "xyplot.points"){
#     grid.garnish(annotationInfo@gridObjId, group=FALSE, grep=TRUE,
#                  class       = class,
#                  onclick     = callbacks[,1],
#                  onmouseover = callbacks[,2],
#                  onmouseout  = callbacks[,3])
#     isok = TRUE
#   }
#   
#   return(list(annotateOK = isok))
# }


renameNodes = function(doc, path, prefix)
  {
    ns = getNodeSet(doc, path, "x")
    if(length(ns)>0)
      {
        oldids = sapply(ns, function(x) xmlAttrs(x)["id"])
        newids = paste0(prefix, "-", oldids)
        names(newids) = names(oldids)

        for(i in seq_along(ns))
          xmlAttrs(ns[[i]]) = newids[i]
        TRUE
      } else {
        FALSE
      }
  }


##--------------------------------------------------------------------------------------
## HTML table to show 'tooltips' for mouseover events
## The function creates a table with 2 columns and as many rows as 'x' has columns.
## The first column will contain the rownames of 'x', the second column will be empty
##---------------------------------------------------------------------------------------
annotationTable = function(x, name) {
  bgcol = rep(c("#d0d0ff", "#e0e0f0"), ceiling(ncol(x)/2))[seq_len(ncol(x))]
  tab  = paste0("<tr bgcolor='", bgcol, "'><td>", colnames(x), "</td><td style='font-weight:bold'></td></tr>\n", collapse="\n")
  tab  = paste0("<table id='", paste("Tab", name, sep=":"), "'>", tab, "</table>")
}