edit

anvio/docs/programs/anvi-draw-kegg-pathways.md

@@ -190,7 +190,7 @@ anvi-draw-kegg-pathways --external-genomes %(external-genomes)s \
 
 As with comparisons of databases rather than groups, the default setting with two or three groups is to color reactions explicitly by the group or combination of groups in which they occur. With more databases, it makes more sense to color reactions by the number of databases in which they occur using a sequential colormap. The option `--colormap-scheme` can be used to override this behavior, e.g., to color reactions by group count rather than explicitly by membership using `--colormap-scheme by_count`.
 
-The following example continues with `Galactose metabolism`, now including two groups of genomic contigs databases from *Enterococcus faecalis* and *Enterococcus faecium*. The program was run three times with different values of `--group-threshold`. The top map has a threshold of 0, so a reaction is included in the *faecalis* group if it has corresponding KOs in any of the six *faecalis* genomes, and included in the *faecium* group if it has KOs in any of the five *faecium* genomes. The middle map has a threshold of 0.5, so reactions in the *faecalis* group must be in at least four of six *faecalis* genomes, and reactions in the *faecium* group must be in at least three of five genomes. The bottom map has a threshold of 1. As in the map grid of *faecalis* genomes from above, the group maps show that some *faecalis* strains may be missing steps from `Lactose` to `D-Tagatose-6P` in the tagatose-6-phosphate pathway, though at least four of the strains have each step. In comparison, a greater proportion of the *faecium* strains have these steps, with all of them having the first two.
+The following example continues with `Galactose metabolism`, now including two groups of genomic contigs databases from *Enterococcus faecalis* and *Enterococcus faecium*. The program was run three times with different values of `--group-threshold`. The top map has a threshold of 0, so a reaction is included in the *faecalis* group if it has corresponding KOs in any of the six *faecalis* genomes, and included in the *faecium* group if it has KOs in any of the five *faecium* genomes. The middle map has a threshold of 0.5, so reactions in the *faecalis* group must be in at least four of six *faecalis* genomes, and reactions in the *faecium* group must be in at least three of five genomes. The bottom map has a threshold of 1. As in the map grid of *faecalis* genomes from above, the group maps show that some *faecalis* strains may be missing steps from `Lactose` to `D-Tagatose-6P` in the tagatose-6-phosphate pathway, though at least four of the strains have each step. In comparison, a greater proportion of the *faecium* strains have these steps, with all of them having the first two, as seen in the bottom map with a threshold of 1.
 
 ![Galactose metabolism group maps using three group thresholds](../../images/anvi-draw-kegg-pathways/kos_db_groups_galactose.png)