Turn on mathjax for some pretty formulae, fixed docstrings.

docs/Doxyfile

@@ -1694,7 +1694,7 @@ FORMULA_MACROFILE      =
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
 # Note that the different versions of MathJax have different requirements with

include/scran_markers/summarize_effects.hpp

@@ -104,7 +104,7 @@ struct SummarizeEffectsOptions {
  * The first dimension is the fastest changing, is of length equal to the number of groups, and represents the first group.
  * The second dimension is the next fastest changing, is also of length equal to the number of groups, and represents the second group.
  * The third dimension is the slowest changing, is of length equal to the number of genes, and represents the gene.
- * Thus, an entry \f$(i, j, k)\f$ represents the effect size of gene $k$ for group $i$ against group $j$.
+ * Thus, an entry \f$(i, j, k)\f$ represents the effect size of gene \f$k\f$ for group \f$i\f$ against group \f$j\f$.
  * @param[out] summaries Vector of length equal to the number of groups.
  * Each entry corresponds to a group and is used to store the summary statistics for that group.
  * Each pointer in any given `SummaryBuffers` should either point to an array of length equal to the number of genes, 
@@ -130,7 +130,7 @@ void summarize_effects(Index_ ngenes, size_t ngroups, const Stat_* effects, cons
  * The first dimension is the fastest changing, is of length equal to the number of groups, and represents the first group.
  * The second dimension is the next fastest changing, is also of length equal to the number of groups, and represents the second group.
  * The third dimension is the slowest changing, is of length equal to the number of genes, and represents the gene.
- * Thus, an entry \f$(i, j, k)\f$ represents the effect size of gene $k$ for group $i$ against group $j$.
+ * Thus, an entry \f$(i, j, k)\f$ represents the effect size of gene \f$k\f$ for group \f$i\f$ against group \f$j\f$.
  * @param options Further options.
  *
  * @return A vector of length equal to the number of groups.