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Using the Data Console

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11.6 Using the Data Console

The Data Console displays information about selected data points or histogram bars in the graph viewer as well as user annotations for all graphs in the Plot Viewer. (See Figure 92, the Data Console is outlined in black.) The data console is shared by all graphs in the Plot Viewer, not specific graphs.

[Picture]

Figure 92: Histograms with Data Console Outlined

There are three tabs in the Data Console, these tabs are:

  • Current
  • History
  • User Annotations

Current Tab

This tab displays information on data points or histogram bars selected in the Graph View. Clicking in the graph view will display information on the nearest point (or histogram bar) to the location selected by the mouse. The type of information displayed depends on the type of graph. New information replaces old information and data is not saved when the Plot Viewer closes.

Right-clicking in the Current tab displays the following options:

  • Copy: Copies the selected text to the clipboard.
  • Copy Link Location: Copies the Web URL to the clipboard.
  • Select All: Selects all text in the tab.

The information displayed for each graph is listed below. Brackets indicate the information will be replaced with the indicated name or value.

  • Numeric Value Plots – No Genetic Position Information:
    • [Graph Item Name]
    • Row: [Row Number]
    • [Row Label Header]:[Row Label]
    • Value: [Y-Coordinate Value]
  • Numeric Value Plots – With Genetic Position Information:
    • Click within Graph View:
      • [Marker Name]
      • [Graph Item Name]
      • Value:[Y-Coordinate Value]
      • Position: chr[Number]:[Genetic Position Number]
      • UCSC - NCBI - Ensembl - HapMap (Hyperlinks for chr# : (position − 250) − (position + 250))
    • Click within an Annotation Track: Fields relevant to the track are displayed.
  • Histograms:
    • Name=[Graph Item Name]
    • Column=[Name of Column Plotted in the Histogram]
    • Interval=[[Bar Start X Position],[Bar End X Position]]
    • Count=[Frequency Count Number]
  • XY Scatter Plot:
    • [Row Label Header]:[Row Label]
    • [Dependent Variable Name]:[Y-Coordinate Value]
    • [Independent Variable Name]:[X-Coordinate Value]
  • Heat Maps – No Genetic Position Information:
    • [Row Label Header] [Row Label] ([Row Index])
    • [Column Header] ([Column Index])
    • Value = [Cell value]
  • Heat Maps – With Genetic Position Information:
    • Click within Graph View:
      • [Row Label Header] ([Row Index])
      • [Column Header] ([Column Index])
      • Value = [Cell value]
      • Position = chr[Number]:[Genetic Position Number]
      • UCSC - NCBI - Ensembl - HapMap (Hyperlinks for chr# : (position − 250) − (position + 250))
    • Click within an Annotation Track: Fields relevant to the track are displayed.
  • LD Plot – No Genetic Position Information:
    • Click on a Marker Flag:
      • Marker Info:
      • [Marker Name]
      • MAF ([Minor Allele]): [Minor Allele Frequency]
    • Click on an LD Value:
      • LD Info:
      • [Left Marker Name]
      • MAF ([Left Minor Allele]): [Left Minor Allele Frequency]
      • [Right Marker Name]
      • MAF ([Right Minor Allele]): [Right Minor Allele Frequency]
      • Markers between: [Number of markers between left and right markers]
      • LD Statistics, either EM statistics or CHM statistics depending on selection
      • List of Haplotypes greater than the display threshold frequency and their EM or CHM Frequencies
    • Click on a Haplotype Block:
      • Either Marker Information or LD Information depending on if the click was on a marker flag or LD value within the Haplotype Block.
      • Haplotype block number, haplotypes greater than the display frequency and their EM or CHM Frequency values.
  • LD Plot – With Genetic Position Information:
    • Click on a Marker Flag:
      • Marker Info:
      • [Marker Name]: chr[Number]:[Genetic Position Number]
      • MAF ([Minor Allele]): [Minor Allele Frequency]
      • UCSC - NCBI - Ensembl - HapMap (Hyperlinks for chr# : (position − 250) − (position + 250))
    • Click on an LD Value:
      • LD Info:
      • [Left Marker Name]: chr[Number]:[Genetic Position Number]
      • MAF ([Left Minor Allele]): [Left Minor Allele Frequency]
      • UCSC - NCBI - Ensembl - HapMap (Hyperlinks for chr# : (position − 250) − (position + 250))
      • [Right Marker Name]: chr[Number]:[Genetic Position Number]
      • MAF ([Right Minor Allele]): [Right Minor Allele Frequency]
      • UCSC - NCBI - Ensembl - HapMap (Hyperlinks for chr# : (position − 250) − (position + 250))
      • Distance: [Distance between markers in kb]
      • Markers between: [Number of markers between left and right markers]
      • LD Statistics, either EM statistics or CHM statistics depending on selection
      • List of Haplotypes greater than the display threshold frequency and their EM or CHM Frequencies
    • Click on a Haplotype Block:
      • Either Marker Information or LD Information depending on if the click was on a marker flag or LD value within the Haplotype Block.
      • Block #[Number]:
      • Chr[Number]:[Start Position]-[End Position]
      • Distance: [Size of the block in kb]
      • Markers: [Number of markers in the block]
      • Haplotypes greater than the display frequency and their EM or CHM Frequency values.
    • Click within an Annotation Track: Fields relevant to the track are displayed.

History Tab

The History tab chronologically lists the information viewed in the Current tab along with the date and time the information was viewed in the Current tab. This information is not saved after closing the Plot Viewer.

Right-clicking in the History tab displays the following options:

  • Clear History: Clears the history tab.
  • Copy: Copies the selected text to the clipboard.
  • Copy Link Location: Copies the Web URL to the clipboard.
  • Select All: Selects all text in the tab.

User Annotations Tab

This tab saves all information typed in the text box after closing the Plot Viewer. Any information from the Current or History tab can be copied and pasted in this tab to be saved for future instances of the Plot Viewer.

Right-clicking in the User Annotations tab displays standard text editing options.

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