Update to multi-axial gating

mutliaxial_gating.md

@@ -35,10 +35,28 @@ Repeat the above instructions in Sections 1. and 2. as many times as are require
 ![](./assets/images/MaG_CurrentPheno.png)
 
 ## 3. Phenotype Assignments
-Once a phenotype is defined in Section 2, they will be added to the Phenotype Assignments table in Section 3. The table details the name of each phenotype in the first column, and the subsequent columns are the min and max values of the markers listed for a given phenotypes. Like the previous table, each cell is editable if finer grain control is desired for a given field. If there is a need to reset the whole table, this can be done by clicking the *Reset data editor* button. 
+Once a phenotype is defined in Section 2, they will be added to the Phenotype Assignments table in Section 3. The table details the name of each phenotype in the first column, and the subsequent columns are the min and max values of the markers listed for a given phenotypes. Like the previous table, each cell is editable if finer grain control is desired. If there is a need to reset the whole table, this can be done by clicking the *Reset data editor* button. 
 
 Once the Assigned Phenotype definitions table is complete, its time to integrate it back into the input dataset. This is done by clicking the *Generate new dataset from the phenotype assignments* button.
 
+As can be seen in the first image below, the number of columns that are generated after assigning phenotypes can make the table very long and hard to read. In order to view all columns, you can use the scroll bar or expand the dataframe using the expand icon in the top right of the table. The expanded view will look like the second image.
+
 ![](./assets/images/MaG_PhenoAssign1.png)
 
-![](./assets/images/MaG_PhenoAssign2.png)
+![](./assets/images/MaG_PhenoAssign2.png)
+
+## 4. New Dataset
+
+Once the new dataset has been generated, columns will be appended to the original dataset with the phenotypes that were generated in the previous step. By scrolling all the way to the end of the dataframe shown in this section, you can see new columns with the new assigned phenotype names. Each cell (row) in the dataset will now also have an entry of '+' or '-' for a given assigned phenotype, denoting if it matches the phenotype criteria.
+
+If there is a need to quickly preview some of these Assigned Phenotypes, that can be done using the utility below the New Dataset table.
+
+![](./assets/images/MaG_NewDataset.png)
+
+From here, the next step is to load this New Dataset in the `Phenotyping` Tab. Navigate to the `Phenotyping` page in the app for the next step.
+
+## Custom Naming of Phenotype Combinations
+
+The `phenotyping` documentation site can provide more detail about the overall use and goals for the `Phenotyping` page, but it has an important connection with the `multi-axial gating`. In addition to a *Load Data* button at the top of the page, there is also a *Load Multi-axial Gating Data* button, which loads the New Dataset dataframe that was produced in the last step of the `Multi-axial Gating` page. 
+
+Once the *Load Multi-axial Gating Data* button is pressed, the normal phenotyping elements are populated, including the Phenotypes Assignments Table, Phenotype Summary Table, and the Phenotyping Scatterplot. You will notice in the Phenotype Assignments table that the species names assigned use the phenotypes from the `Mutli-axial Gating` as markers. This distinction is confusing, and it something that we hope to smooth out in the future. Our ultimate hope is that using this page is another opportunity to assign names to your phenotypes, especially when there is overlap with the phenotyping conditions.