artpoon/bioid

Source files for online resources of Bioinformatics of Infectious Diseases course

bioid's Issues

JS animation illustrating effect of cutting dendrogram on clustering

Problem installing on macOS

When running sudo bundle install:

Running 'compile' for libxml2 2.9.8... ERROR, review '/Library/Ruby/Gems/2.3.0/gems/nokogiri-1.8.4/ext/nokogiri/tmp/x86_64-apple-darwin17/ports/libxml2/2.9.8/compile.log' to see what happened. Last lines are:
========================================================================
  "_libiconv", referenced from:
      _xmlIconvWrapper in libxml2.a(encoding.o)
  "_libiconv_close", referenced from:
      _xmlFindCharEncodingHandler in libxml2.a(encoding.o)
      _xmlCharEncCloseFunc in libxml2.a(encoding.o)
  "_libiconv_open", referenced from:
      _xmlFindCharEncodingHandler in libxml2.a(encoding.o)
  "_lzma_auto_decoder", referenced from:
      _xz_head in libxml2.a(xzlib.o)
  "_lzma_code", referenced from:
      _xz_decomp in libxml2.a(xzlib.o)
  "_lzma_end", referenced from:
      ___libxml2_xzclose in libxml2.a(xzlib.o)
  "_lzma_properties_decode", referenced from:
      _is_format_lzma in libxml2.a(xzlib.o)
ld: symbol(s) not found for architecture i386
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [xmllint] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

• macOS 10.13.3 (High Sierra)
• ruby 2.3.3p222

Failed to embed rtt.html in Trees.md

Apparently mouse pointer isn't being captured:

d3.v3.min.js:1 Uncaught TypeError: Cannot read property 'sourceEvent' of null
    at k (VM15 d3.v3.min.js:1)
    at Object.oa.mouse (VM15 d3.v3.min.js:3)
    at SVGRectElement.<anonymous> (rtt.js:132)
    at SVGRectElement.__onmousemove (VM15 d3.v3.min.js:1)

Rescaling rooted tree is causing all branches to stretch

Only two branch lengths should ever be affected by the repositioning of the root at any given time.
Turn off scaling of rooted tree to the SVG panel.

rooted.js: TypeError

If I drag the root way off the tree into the lower-left corner of the SVG, I get the following error:

Uncaught TypeError: Cannot read property 'x1' of undefined
    at closestEdge (rooting.js:215)
    at SVGRectElement.<anonymous> (rooting.js:146)
    at SVGRectElement.__onmousemove (d3.v3.min.js:1)

Animation proceeds without other problems.

Interactive animation of root-to-tip regression

This should comprise three parts:

1. an interactive plot of a tree in unrooted format - user should be able to drag a point to any location along the tree.
2. a dendrogram style plot of the same tree that updates with placement of root in (1)
3. a scatterplot of distance from root (y) against date of sample collection (x)

Fix sidebar logo and CC statement

Currently the bottom of the site sidebar looks like this:

• I want the octocat logo to be level with the first line of text, and to link to the GitHub repo.
• I want the Creative Commons logos to be on the same line as "CC-BY-SA 2019"

Update NJ animation to display Q matrix

Right now only the distance matrix is being shown. However, we choose which clusters to merge based on another set of quantities that are calculated from these distances. When walking through this animation, it is not clear to the students why A and B are merged first.

Draw rectangular layout of rooted tree

I've got this working for the initial draw, but it's not updating with the points.

Reuse JS code for different charts on the same page

I think using IIFE syntax will help create separate namespaces, but it's not working yet.