Potpourri of graph viz and other improvements

[jayqi]

Lots of changes, but I think they make the reports a lot more user-friendly.

Graph viz

• Removed clustering for orphan nodes. It wasn't really helpful, and it broke all the time. It used the visnetwork::visGroups functionality, preventing other things from using it. Closes node clustering feature has been dropped accidentally #102 as it is no longer #relevant.
• Refactored AbstractGraphReporter to use visNetwork::visIgraphLayout instead of separately explicitly using igraph to compute a layout and passing coordinates to visNetwork. The new implementation is simpler and doesn't require hard-coded aliases to available layouts.
• New function igraphAvailableLayouts returns available igraph layout options.
• Changed defaults for layout and moved some of the options out of AbstractGraphReporter to the specific reporters:
  • AbstractGraphReporter defaults to layout_nicely without visHierarchicalLayout
  • DependencyReporter and InheritanceReporter defaults to layout_as_tree and visHierarchicalLayout
  • FunctionReporter defaults to layout_with_graphopt without visHierarchicalLayout. This seems to work well for large, highly interconnected graphs like function networks tend to be.
• InheritanceReporter will now default to coloring nodes by class type
• Graph viz automatically adds a legend if the node color field specified is a character or factor.
• Added dropdown menu to graph viz that lets you select a node by name. Resolves Add node selection to graph_viz #132.

Misc

• Reverses DependencyReporter and FunctionReporter to have convention dependent -> independent. This is how dependency works in UML. Closes Revisiting the directionality of edges (Nov 2018) #131.
• Adjusted package reports to have responsive width (set to 80%). Set knitr chunks to fill available space.
• Fixed a bug where InheritanceReporter errors out if there are parent classes external to the package.

[jameslamb]

Looks great Jay!! These are really good changes. I love the dropdown to focus on one node.

I have two recommendations:

• don't export that igraph thing, just make it a part of documentation / messages
• you need to update vignettes/pkgnet-intro.Rmd to be sure it's consistent with the new directionality

[bburns632]

@jayqi This is an excellent PR. I love the viz changes, especially the node selection and functional layout changes. The vignette and pkgdown changes render well, but I have some questions on the content before publish.

[bburns632]

Oh @jayqi , and you missed a little edit right here: https://github.com/UptakeOpenSource/pkgnet/blob/master/DESCRIPTION#L9 :)

[codecov-io]

Codecov Report

Merging #143 into master will decrease coverage by 2.02%.
The diff coverage is 53.92%.

@@            Coverage Diff             @@
##           master     #143      +/-   ##
==========================================
- Coverage   86.62%   84.59%   -2.03%     
==========================================
  Files          10       10              
  Lines         897      909      +12     
==========================================
- Hits          777      769       -8     
- Misses        120      140      +20

Impacted Files	Coverage Δ
R/PackageFunctionReporter.R	92.94% <100%> (+0.1%)	⬆️
R/PackageDependencyReporter.R	83.46% <100%> (+0.96%)	⬆️
R/PackageInheritanceReporter.R	73.95% <22.22%> (-5.59%)	⬇️
R/AbstractGraphReporter.R	70.73% <46.66%> (-7.21%)	⬇️

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[jameslamb]

@bburns632 can you take another look at this? I think it's ready to go.

[bburns632]

Yes. Will review again tomorrow.

…

On Mon, Dec 10, 2018, 8:59 PM James Lamb ***@***.*** wrote: @bburns632 <https://github.com/bburns632> can you take another look at this? I think it's ready to go. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#143 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AXZRyyLFS3GjnJ-eUpIR8jJ_gJqzIAeGks5u3x-FgaJpZM4Y_77j> .

[bburns632]

@jayqi excellent edits in the vignette. Thank you for going through the extra trouble there. Great PR.

[jameslamb]

@bburns632 @jayqi I re-reviewed. Looks great!

I re-read the vignette (per @bburns632 's request)...I agree with the recent change. "dependency"-"dependent" language is much clearer than what we had before.

fatntastic job