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Overview

Insights is a page within the PHC where subject data for the entire project population is analyzed and visualized using graphs. Users with the layoutAdmin ABAC privilege can create custom layouts, selecting from various graphs and defining the criteria for data displayed. These layouts can be saved for other users to easily access via a dropdown menu.

Note

To visualize the data of a single subject, click the link to learn how to create a layout for a single subject using the Subjects tab in the sidebar of the PHC.

Upon opening the Insights tab, you'll be presented with a default demographic layout consisting of four graphs representing:

  • Gender
  • Race
  • Living Status
  • Age

Any data from the subjects in your project associated with these four categories is now visualized in graphic form.

Note

This layout cannot be saved or modified. If you create a new layout, this demographic layout disappears. However, deleting all created layouts will return you to this initial demographic layout.

Demographic Layout

Any "unknown" in the graphed data represents any questions/categories that do not have data associated with it. There are two instances of this in the clip above. The first is in the Gender graph where some subjects have "unknown" gender. This appears because they did not provide an answer to the gender question. The second instance is in the Race graph where all responses are "unknown" because the subjects in the project were not asked about their race and thus there is no data associated with this category.

Data from the Life Extend (LX) app may also be viewed in Insights but you must first invite the subject to your organization and they must accept the invite.

Insights Layouts

The Layout Dashboard is composed of custom modules (graphs/charts) displaying the subject data you choose and how you want the data visualized. Layouts can be edited after they have been created, though certain admin permissions are needed to be able to create or edit a layout.

Modules

Click modules to learn more and see the various module types available.

Creating a Layout for all Subjects in a Project

  1. Click the Create Layout button in the blue header at the top of the page. This will open the Manage Layouts page. First Layout Here you can create a new layout, delete a layout, change a layout's name and description, copy a layout, or set a layout as default.

  2. Click the Add Layout icon in the top right of the Manage Layouts screen to add a new layout. (You can create multiple layouts) Add New Layout

  3. Name your layout in the window that opens. Layout Name

  4. Give a description for your layout (optional). This description will only be visible on the Manage Layouts page.

  5. Click the Create button. This will take you to the Manage Layouts page.

  6. Click Done to navigate to a blank layout dashboard where you will add your modules. The name of your newly created layout is visible in the blue header at the top of the page.

  7. To the right of the layout name are two icons:

    • Expand allows you to switch between all layouts available or select Manage Layouts Expand and Edit

    • Edit Layout - allows you access to the Add Module button as well as opens a toolbar with other options to edit your current layout.

  8. Click Edit Layout . This opens the configure tools (Raw edit <>, Discard, Edit, and Close) as well as gives access to the Add Module button (purple circle with a "+").

  9. Click the purple circle to add modules/graphs to your layout.

Edit Layout

Insights Edit Clicking the Edit Layout icon in the blue header of the Insights tab allows you access to the following:

  • Add Module button (found in the bottom right of the screen)

  • Edit Layout Toolbar (opens upon clicking the Edit Layout icon in the header)

    • Raw Edit - Here you can view and copy the JSON code of the current layout. This is helpful if you want to copy a complex layout you created in one project and place a copy of it in another project.

      1. Click the Raw Edit
      2. Click the Copy to Clipboard button at the bottom of the screen with the JSON code.
      3. Click the "X" in the top right corner of the JSON code screen to leave that screen.
      4. Click to a different layout or a layout in a different project.
      5. Click the Raw Edit in this current layout.
      6. Select all the code on the screen(to delete existing layout) or add the copied layout to an existing layout by clicking the screen in the location you want to add the new layout.
      7. Paste the code onto the page using Ctrl+V (Windows) or Cmd+V (Mac) .
      8. Click Save at the bottom of the screen.
      9. It will take you to the Layout Dashboard and will apply any data in the current project that applies to the newly added layout modules.
    • Clear - This will clear your entire patient viewer dashboard.

    • Save Changes - This saves any changes you've made to the existing layout.

    • Cancel - Cancels anything you've added since your last save and takes you out of the Edit Layout menu.

Modules

Modules are the graphs/charts that make up a layout. You can customize each module, determining what data is shown, what subject populations to compare, and what module type you'll use to visualize your data. By default, all subjects will be displayed in the modules in your layout. You can also choose to see the graphs reflect data from a selection of subjects, or a cohort,

There is no limit to how many modules you have in a layout, though some graphs take more time to load.

Modules

The types of modules available for your dashboard include:

It is important to note that your data will not automatically save. It is good practice to save your work often by clicking the Save Changes icon , found in the blue header in the Edit Layout toolbar.

Move, Edit, Remove, and Resize Modules

Each existing module can be adjusted with ease by clicking an icon or a handle.

Module Handles

Move a Module

Each module has a series of dots at the top that acts as a handle.

  1. Go into Edit Layout mode, by clicking the Edit Layout icon in the blue header.
  2. Click and hold the handle to drag and drop your module anywhere in your layout.
  3. Click Save Changes icon in the blue header to save your changes.

Resize a Module

Each module has a resizing handle (a triangle of dots) in the bottom right corner, allowing you to adjust the size of your module.

  1. Be sure you are in Edit Layout mode, by clicking the Edit Layout icon in the blue header.
  2. Click and hold the resizing handle as you stretch or shrink the module to the desired size.
  3. Click Save Changes icon in the blue header to save your changes.

Module Tools

When in Edit Layout mode (by clicking the Edit Layout icon in the blue header), you can see four tools at the top of each module.

Module edit tools

These tools include:

  • Copy will copy the layout to:
    • the current layout (you can then modify module settings if you wish).
    • a different layout (if this is selected the current layout will be saved) - clicking this opens a dropdown menu where you can select which layout within your project you wish to copy the module to. Click Accept. A copy of that module has now been placed in the designated layout.
  • Open module in a full screen window (once open, click the "x" to exit the view).
  • Edit - Allows you to perform edits on the existing module:
    1. In the module you wish to edit, click the Edit Module icon in the top right corner of the module.
    2. Adjust the module settings in the window that opens (options available vary based on module).
    3. Click Preview at the bottom of the module settings window to open a preview window.
    4. If everything looks correct, click Apply to build your chart in the layout.
    5. Click the save changes icon in the blue header to save your changes.
  • Delete module:
    1. Click the in the top right corner of the module you want to remove.
    2. Click save changes icon in the blue header to save your changes.

Graph Viewing Tools

Each Graph has an icon at the top right of the module allowing you to make the graph full screen.

Plotly graphs in the PHC have a mode bar of tools to improve the ease of viewing the displayed data (shown below).

Plotly

Mode bar graph tools include (numbers reference the icons in above image):

  1. Download plot as a PNG
  2. Zoom - Zooming can be performed vertically and horizontally. If graphs are stacked, only the one you zoomed in will change. When graphs are layered, all will zoom in. Double clicking within the part you zoomed will reset the vertical
  3. Pan - lets you grab and drag the plot to change the date range seen
  4. Box Select - allows you to select multiple points
    1. Click and drag your cursor to select your data points within the box
    2. Click View Data - a window opens with info for the selected data points.
  5. Lasso Select - allows you to select multiple points
    1. Click and drag your cursor to select your data points within the box
    2. Click View Data - a window opens with info for the selected data points.
  6. Zoom in - lets you zoom in
  7. Zoom out - lets you zoom out
  8. Reset axes - lets up zoom to include your Axes Range, if this has been set. If it has not been set it zooms to a setting that shows all the viewable data.
  9. Toggle spike lines – when you hover, this drops a dotted line to the x and y axis to see where it lands
  10. Show closest data on hover – shows the one data point you are closest to
  11. Compare data on hover – shows all data points when you hover, if you toggle that off you’ll see the single data point that you are closest to

View Data

On each of the graphs, you can click the View Data button in the bottom left of the module. This opens a new window displaying the data in table form.

View Data

Here you can:

  • Open this window in full screen by clicking
  • Toggle between viewing selected subjects or all subjects
  • Access Cohort actions using all or a selection of the subjects viewed:

    1. Select Subjects you wish to add to the cohort
    2. Click on the Cohort action button
    3. Select from:
      • Create Cohort (makes a new cohort)
      • Add to a Cohort (adds to an existing cohort)
      • Remove from a Cohort (removes the selected subjects from a cohort)
    4. Continue selecting the parameters for your action
    5. Click Update or Create depending on the action chosen
  • Export the data displayed (clicking Export opens a new window where you can select masked or unmasked data export)

  • Access other tabs of PHC - hover cursor on a line to access:
    • Opens Subject Viewer for this subject in a new tab
    • Opens Omics Explorer for this subject in current tab
    • Opens Subject Viewer in current tab to view more details

Module Parameters

Module parameters available differ depending on which module is selected and what is being graphed.

Modules have a default label that is assigned to the x and y axis, but are often not very descriptive. These labels can be customized to better describe what is displayed in the chart.

Customize x and y labels:

  1. Go into Edit Layout mode, by clicking the Edit Layout icon in the blue header.
  2. Click the Edit icon in the top right corner of the module.
  3. Under the General tab of the module, navigate to the X and/or Y axis values.
  4. Add the text for the label you wish to be displayed for that axis.
  5. Click Apply to build your chart in the layout.
  6. When you are satisfied with your chart, click the Save Changes icon in the blue header to save your changes.

If you remove the label, it will revert back to the default label.

Remove Module

To remove a module from your layout:

  1. Be sure you are in Edit Layout mode, by clicking the Edit Layout icon in the blue header.
  2. Click the in the top right corner of the module you want to remove.
  3. Click Save Changes icon in the blue header to save your changes.

Manage Layouts

The Manage Layouts page of Insights is where you can add, copy, or delete a layout, edit the name and description of a layout, or set a layout as the default. The Manage Layouts page can be accessed by clicking the expand icon found beside the current layout name in the blue header. Manage Layouts displays all created layouts for this project.

Layout Manager Options

On this page, you can:

  • Add a new layout by clicking the plus sign at the top right of the page.

  • Admins can set the Default layout by clicking the button to the left of the layout you wish to set as default.

    Note: The default layout is the one new users will be presented with the first time they open Insights. Existing users will be presented with the layout they most recently viewed in Insights.

  • Edit the title and description of a layout.

  • Copy a layout.

  • Delete a layout.

Additional Layouts

Creating additional layouts in Insights allows you to present different sets of data on different layout pages (for example, demographic data layout versus pain rating data layout).

To create additional layouts:

  1. Click the expand icon in the blue header at the top of the page. New Layout

  2. Next, click the Manage Layouts button to open the Manage Layouts page. Layout
Creation

  3. Click the add new layout in the top right of the Manage Layouts screen (see above clip).

  4. Name your layout in the window that opens.

  5. Give a description (optional). This description is only visible on the Layout Manager page.

  6. Click the Create button. This will return you to the Manage Layouts page where you should see all created layouts, including the one you just created.

  7. Click Done. This will take you back to the Insights Dashboard.

  8. Click the expand icon in the blue header at the top of the page to switch to the new layout and begin editing.

    Why make multiple layouts? You may want to display different data depending on who is viewing the data. One layout may be to show patients, another may be used for researchers to compare success of treatments based on genetic mutation.

Copying a Layout

You can copy an existing layout by clicking on the Raw edit icon . This allows you to access the JSON code for the modules on the layout page.

How to Copy a Layout from One Project to Another:

  1. Click the Edit Layout icon in the layout you want to copy.
  2. Click the Raw Edit icon
  3. Click "Copy to Clipboard" at the bottom of the page.
  4. Click the Close icon in the top right corner of the screen to close the Raw edit.
  5. Navigate to the project you want to paste the layout into.
  6. Go into Insights and create a new layout or choose the layout you want to paste the JSON code into.
  7. Click the Edit Layout icon
  8. Click the Raw Edit icon
  9. Select the existing code and delete it (optional) and/or click the cursor on the screen beneath "Configuration JSON" and Ctrl+V (Windows) or Cmd+V (Mac) to paste the copied JSON code.
  10. Click Save at the bottom of the screen. This will show you the same layout using the data in the current project.

    There is also availability to copy a layout in the Manage Layout screen. Here you would duplicate with a copy function.

  11. Clear - Clears the entire layout page. You are presented with the following warning: "Are you sure you want to reset your patient viewer dashboard?"

  12. Save Changes - Saves your progress (use this often). If you click on the Cancel icon before saving your progress, you will lose it all.

  13. Cancel - Cancels anything you've modified since the last time you clicked the Save Changes icon.

To add a module, click on the add button at the bottom right of the screen. It opens a selection window with the following module options:

  • Pie Chart - for general data
  • Bar Chart - for general data
  • Scatter Chart - for general data
  • Line Chart - for general data
  • Oncoprint - for genomic data
  • Heatmap - for genomic data
  • Sample PCA - for genomic data
  • Gene Network - for genomic data
  • Survival Curve - for general data
  • Single Value - for general data

Cohorts

Cohorts are subsets of the whole and are useful for filtering out the data visualized in an Insights graph. Only individuals with the Create Data privilege can create a cohort for the project. An example of a cohort is, "all living men, ages 20-45, that are caucasian, and diabetic". Selecting this cohort will display data from only the subjects in the project that meet the criteria defined in the cohort. Any cohort saved in your project will be available in the Cohort expander in the header of Insights. The cohorts you choose in the Cohorts expander are not saveable, meaning, if you click away from your Insights layout, you will have to click on the Cohorts expander in the header and reselect the cohorts you wish to compare in all of the modules.

In Insights, you can select up to 4 cohorts, or up to 3 cohorts and "all" (all is not a cohort, all is everybody in the project). Selecting more cohorts than what is allowed will cause the last one selected to be rejected with the following message:

"The graph is limited to 4 cohorts."

To resolve this, remove any cohorts needed to comply with the limit.

You can check the cohorts created for the project in the Cohorts tab or by clicking on expand icon for Cohorts in the blue header at the top of the Insights page.

Example of Selecting Different Cohorts in Insights

Cohorts Example

In the clip above, selecting different combinations of the available cohorts and clicking Apply will cause the graphs to redraw to represent the data called forth in the selected cohorts. If you select multiple cohorts, your pie chart modules will draw a pie chart to represent each cohort.

Note: Not all modules can display multiple cohorts. Bar, Scatter, Pie, and Line charts all have the ability to reflect multiple cohorts.

The example below shows a bar graph with three cohorts chosen: All, Living Men, and Living Women. Each cohort is represented by a different colored bar. Cohorts Bar

Filtering

Filter

Filtering using the filter icon located in the header of the Insights tab, is useful when you have a more complicated query than what is offered in Subjects Advanced Filter. This is not often used because the subset it creates is temporary and you cannot create a cohort to be used repeatedly from the subset.

To Perform a Complex Filter Query:

  1. Click the filter icon .
  2. Type a command (for example, patients.demographics.gender=female).
  3. Click Apply Filter.

Note

The more common practice is to use the Subjects Advanced Filter where you can create a complex filter and save it as a cohort to be used throughout your project.


Last update: 2021-07-28