Figure 4.

Two distinct display formats that can be produced using CPG, based on the autophagy pathway in select protists. Panel A: A traditional three-state dot plot representation, similar to that presented in the original publication [25]. White designates not found or absent, black a confident assignment, and gray a lower confidence assignment, in this case lacking phylogenetic support. The plot has some appeal, is clean, but is also large, and lacks functional groupings, making assessment of differential levels of occupancy of the distinct complexes or processes within the autophagy pathway difficult to comprehend, while the plot is also not very compact. Tilda and dotted lines indicate many columns omitted for space reasons. Panel B: Standard CPG format, with each complex represented as a single pie, and the higher order taxon membership colorized. Note that the plot is considerably more compact, and complex occupancy and/or subunit retention clear, even for complexes containing many subunits. Data are taken from ref 24 for illustrative purposes only. Both figures generated with CPG with manipulations in Adobe Illustrator. Note that three state occupancy is not allowed in CPG at present so that gray circles in panel A were manually colored.