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Timelines

Timelines View clinical charts linearly. Arrange by relevant events.

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Overview

Timelines allows users to visualize clinical information linearly (or log) to help establish patient treatment timelines. Patient timelines can be aligned and ordered by different patient events. Timelines can operate over specific events, various patient cohorts and different plotting mechanisms. Buttons and dropdowns in the control bar show or hide different areas of the application.

Timelines
  • Events: Events represent a clinical event in the pateint history. All events in the Timelines widow can be toggled on/off in the events control bar.
  • Patients Events: Are color coded on the graph. Each row is an individual patient. Each dot or line represents an event in that patient’s history. Patient events can be toggled on/off and ordered or aligned by a particular event. To view different ordering or alignments view the Order by or Align by dropdowns.
  • Event Window: Information correlating to a particular patient event is displayed in the Event Window box. To view hover over a dot or line in the graph, information on that particular even will appear in the window.
  • Timeline: Patient event timespan linearly from months to years.
  • Control Bar: Collection of controls that operate over the patient and chromosome areas.
  • Survival Curves: Survival curves correlate to each saved cohort above.
  • Cohorts and Collections: Snapshots of the various collections, either patient or gene (gene coming soon). Different filters include visualizing age at diagnosis, gender, race, ethnicity, vital status or tumor status. Also, includes the ability to save and push cohorts through the various tools. To learn more visit Oncoscape
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Use Cases

Define patient cohorts with particular events

Save and view cohorts with particular patient events

  1. Along the click + drag bars zoom in on the selections.
  2. Select what events show in the graph on the control bar.
  3. Determine what view is most beneficial, log or linear.
  4. Hovering over an event will populate the event windows box.
  5. To save the selections, click the + button on the survival curves box.
  6. Enter a name.
  7. Click Done.

Zoom, order and align different events

Zoom order and align different saved cohorts

  1. Along the click + drag bars zoom in on the selections.
  2. Select what events show in the graph on the control bar.
  3. Use the Align By dropdown to make an alignment selection.
  4. To save the selections, click the + button on the survival curves box.
  5. Enter a name.
  6. Click Done.
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Navigation

Align By
Order By

Provides users the ability to align the chart by a particular event, e.g. birth, drug, status. To apply an alignment other than the default (birth) find the Align By dropdown menu and make a selection.

Provides users the ability to order the events, e.g. birth, drug, status. To apply an alignment other than the default (status) find the Order By dropdown menu and make a selection.

Patient Status
Timescale

Provides users the ability to view patient with status of either alive, dead or both. To apply an alignment other than the default (Only dead) find the Patient Status dropdown menu and make a selection.

Provides users the ability to view events either by log or linearly. To apply an order by other than the default (log) find the Timescale dropdown menu and make a selection.

Display Filter

Provides users the ability to view either all patients for that particular disease set or only selected cohorts. To apply an alignment other than the default (Selected Patients) find the Display Filter dropdown menu and make a selction.


Events

Patient events can be toggled on or off by using the Events box.


Event Window

Patients events can be viewed in detail by hovering over individual colored events. Information relating to the particular event will show in the Event Window.

Drug

Progression

Status



Clear Selection + Reset Zoom

The timeline window can be reset to default by clicking the Clear Selection + Reset Zoom button. Zooming in on event timeline can be achieved by hovering over the timeline window until the crosshairs appear. Using the mouse or trackpad drag the crosshairs to the area of choice.


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Methods

Oncoscape hosts level 3 public TCGA datasets representing gene and patient data downloaded from UCSC Xena. To review this data in depth visit our data API. User planning to publish on the provided data must adhere to all publishing guideline set by the NIH. Datasets in Oncoscape are classified by disease type according to TCGA studies.

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Frequently Asked Questions

How do I find patients with an event of choice?

Using the Events Toggle Menu toggle on or off the different event selctions.


How do I export or print my graphs?

Currently, the export feature is only available on the Spreadsheet tool. Users can push saved cohorts to the spreadsheet tool by clicking the the Analysis Tool button at the top of the screen. Once there click the Export button. An Excel file will get generated.


How do I save my data for a return visit?

All data for selections and cohorts will be automatically saved for a return visit assuming users are on the same computer to login. User logins that allow stored sessions from any device will be deployed in a future release.


How do I zoom in on my event selections?

The timeline window can be reset to default by clicking the Clear Selection + Reset Zoom button. Zooming in on event timeline can be achieved by hovering over the timeline window until the crosshairs appear. Using the mouse or trackpad drag the crosshairs to the area of choice.