updated analytics and visualization docs

docs/analytics/built-in/bipartite-graph.md

@@ -4,48 +4,51 @@
 
     This page is work in progress.
 
-## Bipartite
+## Bipartite Graph
 
-This will allow you visualize Bipartite.
+A Bipartite Graph allows you to visualize the bipartite data effectively. Here CoRA use it to demonstrate the matching specimens and its
+relationships in the form of a bipartite graph.
 
-### Create Bipartite
+The following table shows the required and optional fields to generate a bipartite graph.
 
-Left Sidebar Menu -\> Data Visualization -\> Bipartite
+Attributes  | Required/Optional
+------------| -------------- 
+Relations   | Required
+Bones       | Required
+Side        | Required
+Specimen    | Required
+
+### Steps to generate a Bipartite Graph.
+![](media/bipartite.gif)
 
-In order to create Bipartite, click on the 'Data visualization' on the left navigation bar.
-This will take you to the Data visualization page. 
-This page lists different types of project visualizations that can be used on CoRA.
 
 #### Step 1: Select a relation
+![](media/bipartite-relations-select.png)
 
-After a relation was selected, Bone & Side field will be available.
-There are total 4 relations available:
+Select one from the four (4) association relations based on the requirement. The four (4) association relations available are:
 
 - Pair Matching
 - Articulation
 - Refits
 - Morphology
 
-![Bipartite Search Filter](media/bipartite-filter.png)
-
-#### Step 2: Select a Bone & Search Specimens
-
-After a bone was selected, specimens search will be available. Once you click on the search icon, you can select one or multiple specimens to generate the visualization.
-
-![Bipartite Search Specimen Icon](media/bipartite-search-specimen-icon.png)
-
-#### Step 3: Generate Bipartite
-
-***The bolded fields are required.***
+#### Step 2: Select a bone
+![](media/bipartite-bones-select.png)
 
-*The Italic fields can be multi-select*
+Select the bone type of the specimen from the available list of the bones required for the bipartite graph generation.
 
-- **Relations**
-- **Bone**
-- *Side*
-- ***Specimens***
+#### Step 3: Select a side
+![](media/bipartite-side-select.png)
+Select the bone side from the available dropdown list. After selecting the side click on the 'search' icon to generate the list of specimens based on the options selected previously. The following are the list of sides available:
 
-Clicking on 'Go' button under 'Bipartite', it will bring to to the main page of 'Bipartite' with the filter selection. Once 'Bone' field is selected, the other two filter fields show up. 'Bone', 'Relations' and Specimens' required field, 'Side' is optional for generating the graph. 
+- Left
+- Right
+- Unsided
 
-![Bipartite Visualization](media/bipartite-visualization.png)
+#### Step 4: Select a Specimen
+![](media/bipartite-specimen-select.png)
+Select one or more specimen based on the analytics requirement and click on the 'eye' icon to generate the visualization. Now click on any of the colors on the generation to view the relationship in the specimen selected.
 
+### More Options/Filters
+![](media/bipartite-more-options-filter-select.png)
+Click on the kebab menu icon to view more options  of the list of specimens Found/Not Found for the relation and interact with the visualization.

docs/analytics/built-in/collapsible-tree.md

@@ -6,67 +6,84 @@
 
 ## Collapsible Tree
 
-A collapsible tree can present hierarchical data effectively, here CoRA use it to demonstrate specimens and relationships.
-This will allow you to visualize collapsible tree.
+A Collapsible tree can present hierarchical data effectively. Here CoRA uses it to demonstrate specimens and its relationships in the form of a collapsible tree.
 
-### Create Collapsible Tree
+The following table shows the required and optional fields to generate a collapsible tree.
 
-Left Sidebar Menu -\> Data Visualization -\> Collapsible Tree
+Attributes        | Required/Optional |
+------------------|-------------------|
+ Type             | Required          |
+ Individual Number| Required          |
+ Accession Number | Required          |
+ Provenance 1     | Optional          |
+ Bone             | Required          |
+ Specimen         | Required          |
 
-In order to create Collapsible Tree, click on the 'Data visualization' on the left navigation bar.
-This will take you to the Data visualization page. 
-This page lists different types of project visualizations that can be used on CoRA.
+### Select a type
+![](media/collapsible-tree-type.png)
 
-### Generate Bone
+Select a type (specimen or individual) based on the analytics requirement. Select 'Specimen' based on a bone if a specimen is needed to be analyzed. Select 'Individual' if you want to analyze all the specimens that belong to an individual number.
 
-***The bolded fields are required to generate Bone.***
+### Steps to generate a collapsible tree for 'Type: Specimen'
+![](media/collapsible-tree.gif)
 
-***It is mandatory to choose any one of the optional field to generate Bone***
 
-- **Type(Specimens/Individuals)**
-- Individual Number
-- Accession Number
-- Provenance 1
-- Provenance 2
+#### Step-1: Select accession number
 
+![](media/collapsible-tree-accession-select.png)
 
+Select an accession number to which the required specimen belongs to.
 
-Click the Search Bone button to generate Bone options.
+#### Step-2: Select provenance1
 
-#### Step 1: Select a Type
+![](media/collapsible-tree-provenance-select.png)
 
-Once you select a Type, the rest of the fields will be show and enabled.
+Select the provenance1 to which the required specimen belongs to. Note that choosing provenance1 is optional to generate the collapsible tree.
 
-![Collapsible Tree Select Type](media/collapsible-tree-select-type.png)
+#### Step-3: Select bone
 
-#### Step 2: Select Fields
+![](media/collapsible-tree-bone-select.png)
 
-It is mandatory to choose any one of the optional field to generate Bone.
+Select the bone type of the specimen from the available list of the bones. After selecting the bone type click on the 'search' icon to generate the list of specimens based on the options selected previously.
 
-![Collapsible Tree Select Fields](media/collapsible-tree-select-fields.png)
+#### Step-4: Select specimen(s)
 
-#### Step 3: Select a Bone
+![](media/collapsible-tree-specimen-search.png)
 
-Click the Search Bone button to generate Bone options and select a Bone.
+Choose the required specimens for which the collapsible tree is needed to be generated.
 
-![Collapsible Tree Bone Search Button](media/bone-search-button.png)
+#### Step-5: Generate visualization
 
-#### Step 4: Select a specimen
+![](media/collapsible-tree-specimen.png)
 
-Once a bone was selected, you are able to select a specimen.
+The collapsible tree can be generated by clicking on the 'eye' icon for the selected specimen. The collapsible tree can be further expanded by clicking on a specific relationship node which gives list of all related specimens and clicking on these specimens expands the tree even more by generating the relations of it again and the tree continues to grow.
 
-![Collapsible Tree Select Specimen](media/collapsible-tree-select-specimen.png)
+### Steps to generate a collapsible tree for 'Type: Individual'
 
-#### Step 5: Generate Collapsible Tree
+#### Step-1: Select an individual number
 
-Once a specimen was selected, the generate button is clickable and you will able to get the visualization.
+![](media/collapsible-tree-individual-number.png)
 
-![Collapsible Tree Visualization](media/collapsible-tree-visualization.png)
+Select an individual number that you want to explore.
 
+#### Step-2: Generate the collapsible tree
 
-### Specimens Relationship
+![](media/collapsible-tree-individual.png)
 
-***There are 12 possible 12 relationships***
+Click on the 'eye' icon to generate the collapsible tree. Now click on the necessary accession numbers and provenances to generate the list of specimens in the tree and further click on them similar to the specimens type tree to view the
+relations.
+
+### More Options/Filters:
+
+Click on the kebab menu icon to view more options like removing relations with zero specimens, remove non-required relations and Provenance 2.
+
+![](media/collapsible-tree-more-options.png)
+
+Use the toggle switch to remove relations with zero specimens and simplify the graph. Relations can also be removed individually under 'Selected Relations' based on the requirement. Provenance 2 can be used to further filter the specimens.
+
+### Available Specimen relationships
+
+***There are 12 possible relationships to explore***
 
 - pathology
 - trauma 
@@ -82,3 +99,4 @@ Once a specimen was selected, the generate button is clickable and you will able
 - associations-morphology 
 
 
+

docs/analytics/built-in/hierarchical-clustering.md

@@ -4,4 +4,75 @@
 
     This page is work in progress.
 
+## Hierarchical Clustering
+
+Hierarchical clustering is a data analysis method that builds a hierarchy of clusters by either successively aggregating
+individual data points into clusters (agglomerate approach) or dividing a large cluster into smaller ones (divisive 
+approach), based on their similarity. 
+
+In hierarchical clustering, the data is not partitioned into a particular cluster in a single step. Instead, clusters 
+are formed sequentially, with each step involving the merging of the two nearest clusters at a lower level into a 
+higher-level cluster. This process continues recursively until all data points are clustered into a single group or until 
+the desired cluster structure is achieved.
+
+The following table shows the required and optional fields to generate hierarchical clustering visualization
+
+Attributes        | Required/Optional
+----------------- | -------------- 
+Visualization Type| Required
+Relationship      | Required
+
+### Steps to generate Hierarchical clustering graphs
+
+![](media/hierarchical-clustering.gif)
+
+#### Step-1: Select Visualization type
+
+![](media/hierarchical-clustering-type.png)
+
+Select a type of visualization for the hierarchical clustering. The available visualization types are shown in the below
+table.
+
+Visualization Types |
+--------------------| 
+Icicle              |
+Treemap             |
+Sunburst            |
+Circle Packing      |
+Indented Tree       |
+
+#### Step-2: Select a relationship
+
+![](media/hierarchical-clustering-relationship.png)
+
+Select a relationship that is to be used in the hierarchical clustering.
+
+#### Step-4: Visualization 
+
+After selecting the desired relationship the selected visualization is automatically generated. Each visualization type 
+is interactive and can be changed until the desired output is achieved.
+
+Different visualization types that are generated are shown below.
+
+##### Icicle
+![](media/hierarchical-clustering-icicle.png)
+
+##### Treemap
+![](media/hierarchical-clustering-treemap.png)
+
+##### Sunburst
+![](media/hierarchical-clustering-sunburst.png)
+
+##### Circle Packing
+![](media/hierarchical-clustering-circle-packing.png)
+
+##### Indented Tree
+![](media/hierarchical-clustering-indented-tree.png)
+
+### More Options/ Filters:
+
+![](media/hierarchical-clustering-more-options.png)
+Click on the kebab menu in the top right corner to find more options. These options include filtering the specimens by
+*Accession Number*, *Provenance 1*, *Provenance 2* and a particular *specimen* can also be selected.
+
 

docs/analytics/built-in/index.md

@@ -11,3 +11,4 @@ in experimentation phase until final release. You are encouraged to use the buil
     We would appreciate your use of these analytics and visualizations and your feedback on making them better and more useful to you.
     Thank you.
 
+

docs/analytics/built-in/measurements-scatterplot.md

@@ -5,64 +5,83 @@
     This page is work in progress.
 
 
-The measurements scatterplot can be used to narrow down your search space for likely pair matches. It can be used with any bones 
-that allow for the capture of measurements such as Humerus, Ulna, Radius, Femur, Tibia, etc.
+The measurements scatterplot can be used to narrow down your search space for likely pair matches. It can be used with any bones that allow for the capture of measurements such as Humerus, Ulna, Radius, Femur, Tibia, etc.
 
 !!! note
     Here is a complete list of [bones measurements](../../forensics-anthro-guide/measurements.md)
 
-The measurement scatterplot is useful for identifying or narrowing down for a given specimen which possible specimens are likely
-pair matches that deserve a more closer inspection. You can navigate to the measurements scatterplot screen from 
-Left Sidebar Menu -\> Data Visualization -\> Measurement Scatterplot.
 
-## Generate Measurement Scatterplot
+## Measurement Scatter Plot
+A measurement scatter plot is useful for identifying or narrowing down for a given specimen which possible specimens are likely pair matches that deserve a more closer inspection
+
+The following table shows the required and optional fields to generate a measurement scatter plot.
+
+Attributes        | Required/Optional
+----------------- | -------------- 
+Bone              | Required
+Side              | Required
+X-Axis Measurement| Required
+Y-Axis Measurement| Optional
+Specimen          | Required
+
+
+### Steps to generate a Measurement Scatter Plot.
+![](media/measurement-scatter-plot.gif)
+
+
+#### Step-1: Select bone
+
+![](media/measurement-scatter-plot-bones.png)
+Select the bone type of the specimen from the available list of the bones required for the Measurement scatter plot generation and this will enable other field to show.
 
-***The bolded fields are required.***
-- **Bone**
-- **X-Axis**
-- **Y-Axis**
-- Completeness
 - Side
+- X-Axis Measurement
+- Y-Axis Measurement
+
+#### Step-2: Select side
 
-Clicking on 'Go' button under 'Measurements Scatter Plot', it will bring to to the main page of 'Measurements Scatter Plot' with the filter selection.Pick unique field for filters then the generate button will be working.
+![](media/measurement-scatter-plot-side.png)
+elect the Side to march the bone and the specimen from the available list of the sides.  The following are the list of Sides available:
 
-#### Step 1: Select a bone
+- Left
+- Right
+- Unsided
 
-Once you select a Bone, the rest of the fields will be show and enabled.
+#### Step-3: Select X-Axis Measurement
 
-![Measurement Scatterplot Bone](media/measurement-scatterplot-bone.png)
+Select the X-Axis Measurement for the Scatter plot.
 
-#### Step 2: Select X-Axis & Y-Axis, Other Fields
+![](media/measurement-scatter-plot-x-axis-measurement.png)
 
-'X-Axis Measurement' and 'Y-Axis Measurement' are required field, 'Side' and 'Completeness' optional for generating the graph. You will not able to click on the generate button if 'X-Axis Measurement' and 'Y-Axis Measurement' have same field.
 
-![Measurement Scatterplot Filter](media/measurement-scatterplot-generate.png)
+#### Step-4: Select Y-Axis Measurement
 
-#### Step 3: Click the generate button
+Select the Y-Axis Measurement for the Scatter plot, after selecting the Y-Axis Measurement proceed to click on the 'eye' to generate the scatter plot.
 
-Click the generate button on the right side after fields are selected.
+![](media/measurement-scatter-plot-y-axis-measurement.png)
 
-#### Step 4: Select a specimen
 
-After the generation, you will able to select a specimen and get the visualization.
+![](media/measurement-scatter-plot-generation-1.png)
 
-![Measurement Scatterplot Visualization](media/measurement-scatterplot-visualization.png)
 
-### Get specimen name when hovered over
+#### Step-5: Select a specimen
 
-You will able to get the specimen name, bone, side, X-Axis and Y-Axis when hovered over.
+![](media/measurement-scatter-plot-specimen.png)
 
-### More graph options
+Select one or more Specimen based on the project requirement and click on the 'eye' icon to generate the visualization.
 
-In the menu on the right side, you can see more options on how your measurement scatterplot display and graph detail information.
+![](media/measurement-scatter-plot-generation.png)
 
-![Measurement Scatterplot More Graph Options](media/measurement-scatterplot-more-graph-options.png)
+### More Options/Filters
+![](media/measurement-scatter-plot-more-filters.png)
+Click on the kebab menu icon to view more options to adjust the scatter plot to march the project requirement. The following are available when you click on the 'kebab'.
+
+- Completeness
+- Adjust Target Area
+- DNA (Optional)
 
 ***The bolded fields are selectable.***
 - **Don't show Zero Measured Specimens**
 - **Remove outliers that don't meet min/max**
 - Graph Statistics Analysis
-- Graph Legend
-
-
-
+- Graph Legend