Fleshed out documentation for the intersection argument.

include/singlepp/Intersection.hpp

@@ -18,13 +18,17 @@ namespace singlepp {
 
 /**
  * Intersection of genes between two datasets.
- * Each element is a pair of matching genes and contains the row indices of those genes in each dataset.
- * A row index for either matrix should occur no more than once in this object.
+ * Each pair represents a gene that is present in both datasets.
+ * The two elements of the pair represent the row indices of that gene in the respective matrices.
  *
  * Typically, the first element of the pair contains the row index of a gene in the test dataset,
  * while the second element of the pair contains the row index of the same gene in the reference dataset.
  * This convention is used by `intersect_genes()`, `train_single_intersect()` and `prepare_integrated_input_intersect()`.
  *
+ * A row index for a matrix should occur no more than once in the `Intersection` object.
+ * That is, all the first elements should be unique and all of the second elements should be unique.
+ * Pairs may be arbitrarily ordered within the object.
+ *
  * @tparam Index_ Integer type for the gene (row) indices.
  */
 template<typename Index_ = DefaultIndex>

include/singlepp/train_integrated.hpp

@@ -115,7 +115,9 @@ TrainIntegratedInput<Value_, Index_, Label_> prepare_integrated_input(
  * @tparam Label_ Integer type for the reference labels.
  * @tparam Float_ Floating-point type for the correlations and scores.
  *
- * @param intersection Vector defining the intersection of genes between the test and reference datasets, see `intersect_genes()` for details.
+ * @param intersection Vector defining the intersection of genes between the test and reference datasets. 
+ * Each pair corresponds to a gene where the first and second elements represent the row indices of that gene in the test and reference matrices, respectively.
+ * See `intersect_genes()` for more details.
  * @param ref Matrix containing the reference expression values, where rows are genes and columns are reference profiles.
  * The number and identity of genes should be consistent with `intersection`.
  * @param[in] labels An array of length equal to the number of columns of `ref`, containing the label for each sample.

include/singlepp/train_single.hpp

@@ -295,7 +295,9 @@ class TrainedSingleIntersect {
  * @tparam Label_ Integer type for the reference labels.
  * @tparam Float_ Floating-point type for the correlations and scores.
  *
- * @param intersection Vector defining the intersection of genes between the test and reference datasets, see `intersect_genes()` for more details.
+ * @param intersection Vector defining the intersection of genes between the test and reference datasets.
+ * Each pair corresponds to a gene where the first and second elements represent the row indices of that gene in the test and reference matrices, respectively.
+ * See `intersect_genes()` for more details.
  * @param ref An expression matrix for the reference expression profiles, where rows are genes and columns are cells.
  * This should have non-zero columns.
  * @param[in] labels An array of length equal to the number of columns of `ref`, containing the label for each reference profile.