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Overview

Insights is a layout page within the PHC where subject data can be analyzed and visualized using graphs.

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

The types of modules available for your dashboard include:

  • Pie Chart
  • Bar Chart
  • Scatter Chart
  • Line Chart
  • Oncoprint (visualize gene mutations)
  • Heatmap (gene expression heat map)
  • Sample PCA (gene expression PCA plot)
  • Gene Network (gene expression network plot)
  • Survival Curve
  • Single Value

Creating Your First Layout

  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 in 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 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.

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.

Edit Module

You can reopen the module settings and perform edits on existing modules:

  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. Make corrections to your module settings in the window that opens.
  4. Click Apply to build your chart in the layout.
  5. When you are satisfied with your chart, click the Save Changes icon in the blue header to save your changes.

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.

Pie Charts

Pie Charts are only used for patient demographics. Pie Chart

Add a Pie Chart to Your Layout:

  1. If you are not already in Edit Layout mode, enter it by clicking the Edit Layout icon in the blue header.
  2. Click the Add Module button at the bottom right of the screen.
  3. Select Pie Chart.
  4. In the window that opens, three tabs are available to customize your pie chart: General, Style, and Advanced.

    General

    Pie Charts

    a. Module Name - Name the pie chart to reflect what the chart will represent.

    b. Group Patients by Demographic - Click the dropdown menu and select which demographic you want displayed in the chart (Race, Gender, Living Status, Ethnicity). c. Click Apply to build your Pie Chart or continue editing the colors and margins in the Style and Advanced tabs of the module (see below).

    Style

    The Style tab allows you to adjust the colors of your pie chart. You can also load a palette for more color options.

    Style

    Advanced

    The Advanced tab allows you to adjust the margins of your module, though this function is not commonly used.

    Advanced

  5. When you are done with your selections, click Apply to update the contents of the module. This will take you back to the Layout Dashboard where you can view your new pie chart.

  6. If you are happy with the results, click the Save Changes icon found in the blue header at the top of the page. Or if you need to make changes, click the Edit icon in the top right corner of the module.

Note: Clicking Apply will create your chart. It does not save the layout. Clicking away without saving the layout using the Save Changes icon (found in the blue header) will cause you to lose all changes since your last save.


Bar charts

Bar charts are used to compare categories of data.(e.g., Comparing the number of men vs. women in our subject pool that smoke or vape.) Bar Chart

Add a Bar Chart to Your Layout:

  1. If you are not already in Edit Layout mode, enter it by clicking the Edit Layout icon in the blue header.
  2. Click the Add Module button at the bottom right of the screen.
  3. Select Bar Chart.
  4. In the window that opens, three tabs are available to customize your Bar Chart: General, Style, and Advanced.

    Using data from a previously administered survey, we built a bar chart to display our subjects' responses to an intermittent fasting question and included our input below (in parentheses) for each setting within the module.

    General

    Module Settings - (e.g., Intermittent Fasting) Replace the word "Bar Chart" with a name that reflects what the chart will represent (optional).

    X-Axis - (e.g., Do you Intermittent Fast?) This is what we are grouping by or what we want our columns to represent. This label cannot be changed.

    • Group by Resource - (e.g., Observations) Select the FHIR resource type to group by: Medications, Procedures, Genes, Patients, Conditions, or Observations (Lab values, LX data, Questions, and Survey data are all types of Observations.)

      • Further filtering happens based on the Group by Resource chosen above and includes either Group by Code search box or Group by Property dropdown. (This is the text for the groupings along the X-Axis.)

        • If Group by Resource = Medications, Procedures, Observations, or Conditions - A Group by Codes search bar is available.

          1. Group by Codes - (e.g., Do you Intermittent Fast?) Click in the Group by Codes search box and scroll through options, or type a keyword to search. Once you select something, it will show up as a chip beneath the search bar, showing what you've selected.

          2. Select the Group by Value - (e.g., Observation Values) This is the text displayed that represents the grouping on the X-Axis. Only one selection will work for each survey question, so if you aren't getting your data to graph, try selecting a different option.:

            • Observation Display Values - provide numeric values for the answer
            • Observation Values - provide numeric values for the answer
            • Text Values - provide numeric values for the answer

            These first 3 options are similar but behind the scenes they are coded differently and associated with different data. If your data is not graphing, try a different selection.

            • Quantities - provide numeric values for the answer (e.g., How many people rated their pain a level 5?)
            • Total Observations - show all the responses in one single bar (e.g., "How many procedures have this population had?" would provide a total procedure count.)
          3. If Group by Resource = Patients - a Group by Property dropdown appears where you can select age, gender, race, ethnicity, or patient.

          Note - for "age", you'll also have the option of clicking a checkbox to graph the bar chart as a Histogram (grouping numbers into ranges e.g., ages 0-10, 11-30, etc.)

        • Sort Order - (e.g., Descending) Select between Descending or Ascending to determine the appearance of your chart. (Your chart will only change appearance based on this selection if it's displaying a quantity or numeric response.)

      Y-Axis (you cannot change this label)

      Aggregation Resource - (e.g., Observations) This should be the same as the resource you selected in the X-Axis Group by Resource, so if you chose observation for the X-Axis, choose it here as well:

      • Medications
      • Procedures
      • Observations (LX data, Questions, and Survey data are all Observations.)
      • Patients
      • Conditions
      • Genes

      Aggregation Filter Code - (e.g., Do you intermittent fast?)Only one selection allowed. Again, this should be the same code as what you selected for the X-Axis. Use the search bar to scroll through options, or type a keyword to search. Once you select it, a chip will appear beneath the search bar showing what you selected.

      Aggregation Property: (e.g., Patient) Value Quantity, Value String, Observation, and Patient. Patient is most frequently used.

      Aggregation Function: (e.g.,Count) Standard Deviation, Average, Minimum, Maximum, First Quartile, Second Quartile, Median, Third Quartile, and Count. Count is most frequently used.

      • If you choose "Count", you'll be presented with the Display As dropdown where you can choose to show the data as a Percent or a Count. (Count is more commonly used but when you compare cohorts and one cohort is larger than the other, it's useful to view it as a percent for a more balanced size.)

      • If you choose "Standard Deviation", there are no other selections under the Y-Axis.

      • If you choose Average, Minimum, Maximum, or First Quartile, you can click the Graph with Standard Deviation checkbox.

      Clicking the Graph with Standard Deviation checkbox will show the standard deviation (optional).

      d. Cohort Comparisons

      Cohort Comparison - This sets a default comparison between two cohorts and keeps it as part of the module until you remove it. The bars of your chart will be split to represent the different cohorts in the given module. In the image below, we selected Cohort 1 = Living Men and Cohort 2 = Living Women. By doing this, we can compare how many living men vs. women see a Mental Health Therapist. The graph reflects that of the 4 subjects in our project, 1 man and 2 women see a Mental Health Therapist and only one woman does not.

      Bar Cohorts

      Setting a Cohort Comparison within a module keeps the comparison specific only to this module and remains here until you remove it. But using the cohorts expansion icon in the blue header applies the cohort comparison to all modules in the layout and resets when you click away from the screen. Click here for more information on Cohorts.

      To set Cohort Comparisons for this module only:

      1. Click the Compare Cohorts checkbox.
      2. Set what Cohorts you want to compare from the existing cohorts by choosing Cohort 1 and Cohort 2.
      3. Click the Apply button in the top right of the module settings window. This saves it so anyone who comes to this layout will see those two cohorts compared in that module.

      Note: The Cohorts expander in the header overrides the Compare Cohorts checkbox option in the individual graph module settings. Only a “layout administrator” can modify the cohorts in the module editor where the Cohorts expander in the page header is accessible to all.

      Style

      The Style tab allows you to adjust the colors of your pie chart. You can also load a palette for more color options.

      Style

      Advanced

      The Advanced tab allows you to adjust the margins of your module, though this function is not commonly used.

      Advanced

  5. If you are happy with the results, click the Save Changes icon found in the blue header at the top of the page. Or if you need to make changes, click the Edit icon in the top right corner of the module.

Note: Clicking Apply will create your chart. It does not save the layout. Clicking away without saving the layout using the Save Changes icon (found in the blue header) will cause you to lose all changes since your last save.

Bar Compare

As seen in the image above, the bar chart on the left shows the data as a Count and the one on the right shows the data as a Percent.


Single Value

Single Value

Single Value or Count calculates a single value number for procedures or observations (e.g., 5 women in our project are pregnant).

  1. If you are not already in Edit Layout mode, enter it by clicking the Edit Layout icon in the blue header.
  2. Click the Add Module button at the bottom right of the screen.
  3. Select Single Value.
  4. In the window that opens, continue customizing your Single Value Module.

    General

    • Title and Description

      • Title: Name your project (this is placed at the top of the module - in the example above, we named it Pregnant)
      • Description: This will be displayed below the numeric value. The description tells what the count/value represents (e.g., # of pregnant women in the project.)
      • Description size (small, medium, large): This determines the size of your font.
    • Category

      • Type: Choose between procedures or observations (Observations typically has more data).
        • Procedures (e.g., fasts)
        • Observations - include survey questions
      • Group by Code (only 1 code allowed): Click the search box, type a known medical code/procedure name or any letter to search through the codes and names associated with those codes as well as survey questions asked within the project. (e.g., Are you pregnant?)
    • Value:
      • Source - This is what you want to count (e.g., patients).
        • Procedures - total number of procedures that exist within the project (i.e., this number would tell us how many fasts/procedures in total were recorded by everyone within the project)
        • Patients - counts the number of patients that meet the observation you are counting (e.g., # of women pregnant in the project)
        • Observations (e.g., Are you pregnant?)
    • Property - Choose between Patient or Observation (e.g., Patient).
    • Function - Count (no other option)
    • Value Color - Select the color of the number displayed (black, blue, green, red, yellow)
    • Click Apply in top right corner of module settings box.
  5. If you are done modifying the module, click the Save Changes icon found in the blue header at the top of the page. Or if you need to make changes, click the Edit icon in the top right corner of the module.

    Note: Clicking Apply will create your chart. It does not save the layout. Clicking away without saving the layout using the Save Changes icon (found in the blue header) will cause you to lose all changes since your last save.


Scatter Chart

Scatter Charts are used to compare two variables within a set of data (e.g., comparing body weight to the # of days the subject exercises 30+ minutes).

To create your Scatter Chart:

  1. If you are not already in Edit Layout mode, enter it by clicking the Edit Layout icon in the blue header.
  2. Click the Add Module button at the bottom right of the screen.
  3. Select Scatter Chart.
  4. In the window that opens, three tabs are available to customize your Scatter Chart: General, Style, and Advanced.

    Insights Scatter

    The settings we used in our module to build the above Scatter Chart will be noted in parentheses next to each setting below.

    General

    Module Settings

    • Name your Scatter Cart - This will be at the top of the module. (e.g., Current Weight vs. # Days Workout 30min+)

    X-Axis

    Aggregation Resource - (e.g., Observations) Patients, Observations, Conditions, Procedures, or Medications

    • An Aggregation Resource of Patients will present you with two dropdowns to further filter your results:

      1. Aggregation Property - Age, Gender, Race, Ethnicity, or Patient

      2. Aggregation Function - Count is the only available option

    • An Aggregation Resource of Observations, Conditions, Procedures, or Medications will present you with the following:

      1. Aggregation Filter Code - (e.g., What is your current weight?) Only one selection allowed. Type the medical code or a letter in the search box to search for the available filter codes.

      2. Aggregation Property correlates with your filter code - (e.g., Value Quantity) Value Quantity, Value String, Observation, or Patient

      3. Aggregation Function - (e.g., Average) Standard Deviation, Average, Count, Minimum, Maximum, First Quartile, Second Quartile, Median, or Third Quartile

    X Axis Sort Order - Ascending or Descending

    Y-Axis

    While the options for the Y-Axis are the same as the X-Axis, your selections for the Y-Axis should differ from the X-Axis because Scatter Charts compare two variables in a set of data.

    Aggregation Resource - (e.g., Observations) Patients, Observations, Conditions, Procedures, or Medications

    • An Aggregation Resource of Patients will present you with two dropdowns to further filter your results:

      1. Aggregation Property - Age, Gender, Race, Ethnicity, or Patient

      2. Aggregation Function - Count (only available option)

    • An Aggregation Resource of Observations, Conditions, Procedures, or Medications will present you with the following:

      1. Aggregation Filter Code - (e.g., How many days a week you workout for 30+minutes) Only one selection is allowed. Type the medical code or a letter in the search box to search for the available filter codes.

      2. Aggregation Property this correlates with your filter code - (e.g., Value Quantity) Value Quantity, Value String, Observation, or Patient

      3. Aggregation Function - (e.g., Average) Standard Deviation, Average, Count, Minimum, Maximum, First Quartile, Second Quartile, Median, or Third Quartile

    Style

    The Style tab allows you to adjust the colors of your pie chart. You can also load a palette for more color options.

    Style

    Advanced

    The Advanced tab allows you to adjust the margins of your module, though this function is not commonly used.

    Advanced

  5. If you are happy with the results, click the Save Changes icon found in the blue header at the top of the page. Or if you need to make changes, click the Edit icon in the top right corner of the module.

Note: Clicking Apply will create your chart. It does not save the layout. Clicking away without saving the layout using the Save Changes icon (found in the blue header) will cause you to lose all changes since your last save.

Viewing the Scatter Chart

Each point on the scatter plot is an individual response. You can zoom in, or click on an actual data point and get it's x and y coordinates. Zooming side to side allows you to zoom in on one axis. To zoom back out to the original view, double tap on that module.

On the scatter plots you can click "View Data" in the lower left corner of the module to open a window and list the data.


Line Charts

Line charts show you values over time.

To create your Line Chart:

  1. If you are not already in Edit Layout mode, enter it by clicking the Edit Layout icon in the blue header.
  2. Click the Add Module button at the bottom right of the screen.
  3. Select Line Chart.
  4. In the window that opens, three tabs are available to customize your Line Chart: General, Style, and Advanced.

    Insights Line

    Module settings used to create the above chart are in parentheses in the settings below. General

    Module Settings

    • Name your Line Chart (e.g., Avg. Weight Trend in the Population)

    X-Axis

    X-Axis Time Series

    • Time Series Interval - (e.g., day)Day, Month, or Year
    • Time Series Resource - (e.g., Observations) Observations, Medications, Procedures, or Conditions

    Interval Code Relation (e.g., after first occurrence):

    • After First Occurrence of Code is the most commonly used option. This selection sets everyone to the same day 0. This might be used if you are running a 12 week program and have individuals starting on different start dates. This allows you to evaluate their progress over 12 weeks regardless of their start date.
    • Before Last Occurrence of Code
    • Before First Occurrence of Code
    • After Last Occurrence of Code - e.g., after the last biopsy

    Time Series Code - What do we want to measure? (e.g., body weight)

    Y-Axis

    • Aggregation Resource (e.g., Observations) Medications, Procedures, Genes, Conditions, Observations, or Patients
    • Aggregation Property - (e.g., Value Quantity) Value Quantity, Value String, Observation, or Patient
    • Aggregation Filter Code - (e.g., body weight) Only one selection allowed. Choose the same Filter Code you chose in the X-Axis Filter Code.
    • Aggregation Function - (e.g.Average - shows average body weight of all patients in project on one line as it changes daily over time) Standard Deviation, Average, Count, Minimum, Maximum, First Quartile, Second Quartile, Median, or Third Quartile

    Graph with Standard Deviation checkbox - Select this to see the standard deviation.

    Group Series Data checkbox - Checking this box will graph your data using multiple colored lines, each representing a different subject. A key for the chart will be on the right of the module and includes the subject id and correlating line color.

    • Series Data Grouping Resource - (e.g., Patients) Medications, Procedures, Observations, Conditions, or Patients

    • Series Data Group Property - (e.g., Patient) Age, Gender, Race, Ethnicity, or Patient

    Style

    The Style tab allows you to adjust the colors of your pie chart. You can also load a palette for more color options.

    Style

    Advanced

    The Advanced tab allows you to adjust the margins of your module, though this function is not commonly used.

    Advanced

  5. If you are happy with the results, click the Save Changes icon found in the blue header at the top of the page. Or if you need to make changes, click the Edit icon in the top right corner of the module.

Hiding an Individual Subject from the Line Chart - On the right side of the line graph is a key that shows which colored line goes with each subject id. If you click one of those lines within the key, it will hide that individual's data. This is useful if one person erroneously entered their data using the wrong measurement and skewed the graph.


Survival Curve

Survival Module Settings

Module Name - Give the module a title (e.g., 5 year survival from Last Chemo)

Start - When do we want to start tracking whether or not people are dying?

  • Resource type: (e.g., Observations) Procedures, Observations, Medications, or Conditions

  • Either search for Resource Code - only one allowed (e.g., Chemo) or Click the Select from Project Tags checkbox and select the tag.

  • Reference to Resource - (e.g., After First Occurrence - this means when people started Chemo)

    • After Last Occurrence

Death/Event

Resource Type - (e.g., Date of Death) Medications, Procedures, Conditions, or Observations

Censoring Censor last known follow-up checkbox - Most recent Observation, Condition, Procedure, or Medication is used as the default "last known follow-up date".

Either search for the Resource Code - only one selection allowed by clicking in the search box to look through the codes or click the Select from Project Tags checkbox and select the tag.

Reference to Resource - First occurrence or last occurrence

Duration of Analysis - (e.g., 60 months) Select the number and time interval - days, weeks, months, or years.

Compare Survival Curve across Cohorts checkbox - allows you to select a few cohorts to show by default.

If you are happy with the results, click the Save Changes icon found in the blue header at the top of the page. Or if you need to make changes, click the Edit icon in the top right corner of the module.

Note: Clicking Apply will create your chart. It does not save the layout. Clicking away without saving the layout using the Save Changes icon (found in the blue header) will cause you to lose all changes since your last save.

Viewing your Survival Curve

Survival Curve

The display always starts at 100%. Each stair step down represents someone's death.

Beneath the Survival Curve graph are two buttons:

  • View Data (shows Event Time, Deaths, Censored, No. at Risk, and Survival Probability for each Cohort)
  • View Statistics - shows the following possible data depending on the comparison you run:
    • Cohort:
      • Total
      • Censored
      • Deceased
      • Median Survival
      • Median 95% Confidence Interval
    • Test:
      • Chi-Square
      • Degrees of Freedom
      • Significance
    • Cox Regression Covariates:
      • Risk Ratio
      • 95% Confidence Interval
      • Significance

Manage Layouts

The Manage Layouts page of Insights 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 (e.g., 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

Layout Edits

Configure the Layout: Click on the expand icon for Layout in the blue header at the top of the page. This will open the editing tools (Raw edit <>, Discard, Edit, and Close) Select the Layout page you want to configure. You will see a blank screen. Click the Edit Layout icon in the blue header at the top of the screen. Select the edit layout icon in the blue header at the top of the page. Click the plus sign at the bottom right of the screen to add a module.

Edit layout If you have permission to edit layouts you can modify, add, or subtract layouts: Click the Edit Layout icon. Each module (type of data display) there is an edit button.

Filtering

Filter

Filters do not create a cohort, rather, they are a temporary subset. This is a way to get a more complicated query than what is offered in the current subject search. You can filter your results by clicking the filter button and typing a command e.g., patients.demographics.gender=female or selecting subject tab in a project/subject filters/advanced/add query/typing command e.g., patients.demographics.gender=female).

Filtering is not often used. The main difference between typing the command using the filter button on the Insights page and using the advanced subject filter on the Subjects page is the Filter is temporary while the Advanced subject filter can be saved as a cohort. On the advanced subject filter, you can click "Show Help" and you will be provided with examples of commands to help your query.


Last update: July 10, 2020