metacoder 0.1.3

Mostly minor improvements and bug fixes. Larger changes are waiting on the taxa package to be done, which will be the new home of the taxmap class and the associated dplyr-like manipulating functions like filter_taxa.

Improvements

• Provided helpful error message when the evaluation nested too deeply: infinite recursion / options(expressions=)? occurs due to too many labels being printed.
• heat_tree: improved how the predicted bondries of text is calcuated, so text with any rotation, justification, or newlines influences margins correctly (i.e. does not get cut off).
• heat_tree: Can now save multiple file outputs in different formats at once

Minor changes

• heat_tree now gives a warning if infinite values are given to it
• extract_taxonomy: There is now a warning message if class regex does not match (issue #123)
• heat_tree: Increased lengend text size and reduced number of labels
• extract_taxonomy: added batch_size option to help deal with invalid IDs better
• Added CITATION file

Breaking changes

• The heat_tree option margin_size funcion now takes four values instead of 2.

Bug fixes

• heat_tree: Fixed bug when color is set explicitly (e.g. "grey") instead of raw numbers and the legend is not removed. Now a mixure of raw numbers and color names can be used.
• Fixed bugs caused by dplyr version update
• Fixed bug in heat_tree that made values not in the input taxmap object not associate with the right taxa. See this post.
• extract_taxonomy: Fixed an error that occured when not all inputs could be classified and sequences were supplied
• Fixed bug in primersearch that cased the wrong primer sequence to be returned when primers match in the reverse direction
• Fixed a bug in parse_mothur_summary where "unclassified" had got changed to "untaxmap" during a search and replace
• Fixed outdated example code for extract_taxonomy
• Fixed a bug in mutate_taxa and mutate_obs that made replacing columns result in new columns with duplicate names.