Todo.xml

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<topics xmlns:r="http://www.r-project.org">
<title>SVGAnnotate</title>

<topic>
<items>

<item>
export getShape
</item>

<item>
The class rectangle should be named "Rectangle"?
Comes from guessSVGShape, not getShape
</item>

<item>
Functions for matplot.
</item>

<item>
export addLink()
</item>

<item>
Functions for annotating bar plots,  pie charts, mosaic plots.
<br/>
See tests/barplot.R, tests/piechart.R
</item>

<item>
Optionally identify plot-region nodes as decoration/annotation groups
from drawing lines, text, symbols, circles, etc. on an existing plot.
<br/>
This is a little trick as using layout for example with an inset
could lead to a new plot being inside another.
We can look for one just after a regular plot region.
All somewhat ad hoc and can be erroneous.
<br/>
Allow getPlotRegionNodes() to optionally determine what is an
annotation group (isAnnotationGroup()) and 
return these or omit them.
</item>

<item>
Deal with missing value for the time period for an observation.
Want it to appear when the value becomes available.
But we need an SVG element corresponding to that point.
Add it as an invisible object at the first real point.
But hide it and add material to make it visible at that time.
<br/>
If given the entire data, we can find these missing values
in time == 1 and add these points. Want caller to be able
to say no. The difficulty is that they may want to control
the appearance of those points.
</item>

<item status="done">
Do we need to set the namespace on all the new nodes.
Not if we serialize the SVG. But if we want to do other 
getNodeSet() operations, we will miss those.
Yes, we have to and we have.
</item>

<item status="done">
Get the namespace on the rect that we add on windows to have the right
value.
</item>

<item>
For animations with pch not a circle, get the scaling
for the "radii" right. See gm2.R but add the radius to the call.
</item>

<item status="done">
groupByPch should be able to handle taking a pch as a letter.
<br/>
It is a real problem that we cannot readily solve (although
we could use a list() to separate the characters and integers) as 
pch = c(0, "A") in R of course reads as c("0", "A")
and R won't allow a list.
<br/>
Issue a warning if there are any 0:25 elements in the string.
</item>

<item status="done">
Set/Configuration for Windows, i.e. use Cairo package.
<br/>
Also  works on Unix.
And added a --with-cairo-package argument for configure
to allow overriding using the built-in version.
</item>

<item status="done">
Test in gm4.R and snowflake. Not going in the right spots.
Bounding box of this object?
</item>

<item status="done">
groupByPch() may have to remove the type = 'plot-point' attribute for
the nodes if they were added via a getPlotPoints() call.
Put it on the &lt;g&gt; node.
Also put the pch on the g node too.
</item>

<item>
When we addTypes in getPlotPoints(), we may be wrong!,
e.g. mark a line as a plot-point. 
<br/>
See tests/gm1.R
and then getPlotPoints(pp)[[2]].
These are lines.
<br/>
getBoundingBox and guessPathShape() can determine the actual type
but somewhat expensive.
We have the code isInside() and isAnnotationGroup()
that can determine these things. Just need to know when to do
it.
</item>



<item status="check">
addLink() should allow a style, either inline or class
and should add the CSS if necessary.
<br/>
style  added. <br/>
CSS needs to be.
</item>

<item status="done">
When animate() has a begin that is greater than 0, 
the points don't appear until that time.
<br/>
Add a no-op animateMotion to move each point to its
current location at time 0 for 0 seconds.
</item>

<item status="done">
When we use a different plot symbol, 
getPlotPoints() doesn't get things right.
Returns the wrong thing!
So we need to look at the locations.
<r:code>
doc =svgPlot({
               plot(1:10, pch = "+", col = "red")
               abline(h = 5.5)
               abline(v = 5.5)
             })
getPlotPoints(doc)
</r:code>
<br/>
See tests/shapes.R for finding which ones
correspond to multiple path elements that
appear as many points.
These are 
<r:code>
pch =  3  4  7  8  9 10 11 12 13 14
</r:code>
These all involve multiple lines.
<br/>
We can provide a function that takes the pch 
values used in the plot and regroups.
It is called groupByPch().
</item>

<item>
[Check] When we annotate an SVG document, the
functions for finding components of the plot, e.g.  getPlotPoints(),
fail because of the extra content.
<br/>
Shall we add an argument (that has a default that checks whether there have been annotations).
<br/>
Some of the functions now check for the type attribute.
<r:code>
doc = svgPlot(plot(1:10))
addToolTips(getPlotPoints(doc), 1:10)
getPlotPoints(doc)
</r:code>
works.

<r:code>
doc = svgPlot(plot(1:10, pch = 8))
groupByPch(getPlotPoints(doc), 8)
length(getPlotPoints(doc))
rr = getPlotRegionNodes(doc)  # works
xmlSize(rr[[1]])
</r:code>
Works now.
<br/>
See tests/repeat.R for testing 
</item>


<item status="done">
Check animate works when the points are not "circles"
<br/>
Try passing the points explicitly. See tests/gm2.R
<br/>
Works for points with single paths.
See gm2.R for groupByPch() to handle other pchs.
</item>

<item status="done">
Add radii as a parameter to the animate function and use the code in gm.R to implement
changing the radii if it is passed as an argument.
</item>

<item>
Provide an example of using the hook in animate().
</item>



<item status="done">
Deal with missing values properly in animate(),
i.e. keep them but don't add a motion. Stay where they are.
<br/>
This is done, but  the case  where the first
of the subsequent is now done too, but separately.
We use the location of the point.
<br/>
See tests/animNAs.R
</item>


<item status="done">
Function to convert path for points to circle nodes.
<br/>
Have the code in animation. Just need to make a separate function.
<br/>
Named  pathToCircle()
</item>


<item status="done">
Consolidate the animate() examples.  Use the ones with lines.
tests/gm1.R seems the right one.
<br/>
I put this into animate.Rd
</item>

<item status="done">
animate() is getting the coordinates in SVG space wrong.
See tests/gm1.R. The points should all end up on the horizontal line at 6.
<br/>
It is the problem that xlim and ylim are not the actual limits.
Need xaxs = "i" and yaxs = "i" in the settings.
<br/>
Another approach is to plot all the points
in the order of time and then
post-process the plot to find the coordinates
of these transition points, remove the nodes
but use their coordinates in the animateMotion elements.
See tests/animateMultiPlot.R for an example.
<br/>
Does the problem have anything to do with pixels and points?
Or are we off by some amount from the interior/exterior
of a rectangle. Or is R doing some computations
differently to locate the initial points.
</item>



<item status="low">
Put panel levels into the lattice information.
Put on plot region nodes or in the meta-info header r:graph node?
or both?
<br/>
We have the tools to get these labels from the lattice object.
Instead of putting them in the nodes at the moment, we
serialize the lattice object at the end of the SVG 
document.
</item>

<item>
If possible, write the usr information to each 
plotting region.
<br/>
If we ran this through our RGraphicsDevice,
we could catch frame()/plot.new()
and get the usr information before we change it.
</item>

<item>
JavaScript functions for converting from pixels to data coordinates.
<br/>
With a plot region, panel of a lattice plot, etc.
Need xlim and ylim. Have this for lattice.
<br/>
Can get this from the usr setting on r:display.
</item>

<item status="done">
Implement the guessPathShape function to be able to determine if
a path is rectangle, circle, etc.
<br/>
For the most part, this is done as getBoundingBox() 
does all the work with support from all the help functions
to recognize shapes.
Look at the class of getBoundingBox().
</item>

<item>
getRect should do something more intelligent for Cubic Bezier curves.
<br/>
Should be using getGeneralPath and getBoundingBox.
<br/>
Not sure why we are exporting this?
</item>

<item status="check">
Make getBoundingBox() more intelligent and allow it to work
on a g element with sub-elements, e.g. path, and
<br/>
Done for most, but empirical. May find other types of nodes.
</item>

<item status="done">
At least warn, if not fix, that getBoundingBox()
only works for rectangles and not complex shapes/paths
such as circles and bezier curves.
</item>




<item status="done">
Allow animate() take a character as which to identify the column.
</item>

<item status="done">
addToolTips on the plot points is not getting addArea correct.
</item>

<item status="done">
Do we need addAxesLinks() and addLink()?
<br/>
At the very least, the former should be implemented by calling the latter!
Currently diverging and addAxesLinks is probably being left behind,
e.g., w.r.t. addArea.
</item>

<item status="done">
addAxesLinks() in tests/href.R is not getting the addArea 
correct.
</item>

<item status="done">
Provide methods for addLink() like addToolTips().
<br/>
Doesn't make sense for the document as a whole.
</item>


<item status="done">
Plot regions with tooltips are appearing all black.
Need to sort out CSS, ...
<br/>
First example in tests/panelHRef.R
<br/>
No tootlip entry in the CSS. And tooltip was misspelled
in one default argument as tooltup
</item>

<item status="done">
addLink's addRectangle argument should be addArea.
And make the return value invisible.
</item>

<item status="done">
Function for adding tooltip (and href) 
for a plot region, a panel, a strip, ...
<br/>
For a strip, we don't want/need to addArea.
We can tell this  from the type=strip on the node.
But how do we tell whether the caller specified addArea = TRUE
or if this is the default? Set the default to NA.
<br/>
I have put this into addToolTips() and 
created a function needToAddArea() which takes
the node and the value of addArea given in the call .
</item>

<item status="done">
Get the CSS to work for opera and firefox 
so that a &gt; rect appear transparent.
<br/>
Need to explicitly add the fill attribute to 
the background color of the canvas for Firefox to work

</item>

<item status="done">
addAxesLinks take a style attribute which
can be a name or an inline style (or NA)
</item>

<item status="done">
Break the identifyLatticeElements function into pieces.
<br/>
Now in identifyLatticeElements.R in separate functions.
Checked with findGlobals() to ensure all variables are present.
</item>

<item status="done">
addCSS() should check whether it is already there.
</item>

<item status="check">
For a lattice plot, add meta-information describing the plot,
e.g. legend, labels, axes, observation indices, number of panels,
number of strips/levels within each conditioning factor.
</item>

<item status="check">
addTooltips should allow the user to specify that we should add
a rectangle "underneath" to expand the click region.
And if they do that, specify  a CSS style specification that is inlined,
i.e. a style parameter.
<br/>
Actually it does (useRectangle), but the default value is
no if it is not text.
And the default is computed in methods that are not appropriate,
i.e. if we call addToolTips(doc, tips), useRectangle is computed
in the XMLInternalDocument method and explicitly passed
down through the method calls. But the default has been computed on the wrong 
thing.
So caller has to specify it explicitly.
</item>

<item status="done">
Find the function to put a rectangle behind 
text to allow the onmouseover etc to work on the whole thing.
<br/>
It is in addTooltips.XMLInternalnode .
Now in addAreaTooltip
</item>

<item status="done">
getLatticeLegendNodes()
<br/>
Need to understand what strip.default is producing.
</item>

<item status="done">
getPlotPoints should be able to work on 
an XMLInternalNode returned from 
getPlotRegionNodes().
Currently throws an error.
<r:code>
 doc = svgPlot({
                par(mfrow = c(3, 1))
                plot(mpg ~ wt, mtcars)
                hist(mtcars$mpg)
                plot(mpg ~ disp, mtcars)
               })

  plots = getPlotRegionNodes(doc)
  length(plots)	       
  getPlotPoints(plots[[1]])
</r:code>

getPlotPoints(doc) gives back just the first one.

</item>


<item status="done">
Implement getStripNodes
<br/>
Works for continuous variables, i.e. shingles.
Not recognizing strips for factors.
Seems done. Close, but have to tie up the loose ends which is the
after strip rectangle. Should we re-parent it for the convenience of later post-processing?
</item>

<item status="done">
Annotate the strips with the variable and its level if we have this info
from the lattice object.
<br/>
See tests/latticeStrips.R for different types of variables: shingles and regular factors.
</item>

<item status="check">
findJScripts shouldn't expand name of file in the current directory.
Leave it local.
</item>

<item status="done">
Check svgPlot outputs the entire R command in the r:graph
See latticeLegend and the multiple panels example in tests/
</item>

<item status="done">
Work on the highlighting of paths in 
graphvizDot.svg and graphvizDot.R
<br/>
Is the problem that the curved edges are not getting
highlighted and unhighlighted because we are working
on the g and not the path node. Do we have to
descend into the children.
<br/>
No as we are also highlighting the wrong edges.
<br/>
Issue was we were grouping the nodes, but adding
the new node to the end of the child list
not back in the same  place.
So I added the indexOfNode function in
the XML package so we can use that
with the at parameter in newXMLNode().
</item>

<item status="done">
Function for identifying common style values and
putting them into a CSS file and setting
classes on the SVG nodes.
<br/>
See compressStyles(). Better name that
says convert styles to CSS.
</item>

<item status="done">
High-level function for converting CSS style attribute in SVG node
to sequence of separate attributes.
<br/>
See methods for convertCSSStylesToSVG.
</item>


<item status="done">
Fix up the svgPlot mess with lazy evaluation 
being done eagerly because of method dispatch.
</item>

<item status="done">
Function to manipulate the style elements,
break it up, replace elements and write it back
as a single attribute.
<br/>
See getStyle, modifyStyle, setStyle
</item>

<item status="low">
For the cases where we put lots of curves or sets of points into 
a plot to animate or allow interaction, 
add some AJAX-like material to download individual curves or sets of points
when that particular "group" is needed.
This will avoid big files and allow for lots of little downloads on
demand.
<br/>
Look into doing this for the Election results example (with the pie charts).
</item>

<item status="done">
Adding clickable links to plots
<br/>
on the points and on the axes-labels (done).
</item>

<item status="done">
Allow the tooltips and hyper links to work in the interior
and not just on the path!
</item>




<item status="low">
(Not exported currently)S
getPlotRects (need to export)
is returning back twice as many results
for mfrow.svg and they are duplicates.
<br/>
The problem is that the mfrow() is of density plots
and they have a reference line at the bottom of the plot.
It is in the plot region. But our filtering is including
these.
</item>

<item status="low">
Abstract animation for US elections over year to be used elsewhere.
Give me a data structure of
times with element ids and values to change and tell me what to
change and the loop can do what it does now.
<br/>
Hidden objects over time. Add a reset  previous to hidden.
</item>


<item status="low">
Add legend to the animation example tests/anim.R
to show the colors of the weekdays by name.
<br/>
Partially done in a different way.
</item>


<item status="low">
Why does the original plot not show in anim.R but is colored
<br/>
For the moment, just display the day of the week as a text node.
</item>

<item status="low">
Persistence in linking.
<br/>
When you click on a point, it stays highlighted.
Need to be able to unclick to toggle state
(or reload).
</item>

<item status="done">
Linking for pairs plots. 
</item>

<item status="done">
Add tooltips to points
</item>

<item status="done">
Do the show/hide  example for the European
exchange rate in lattice.
First put in long form.
Condition on year and group by currency.
Then work through the panels and give ids
for each panel
<br/>
See file://localhost/Users/duncan/Books/XMLTechnologies/Rpackages/SVGAnnotation/tests/euSeries4.svg
</item>
</items>
</topic>
</topics>