The following table lists the parameters in the Scatter Plots view.

Parameters in the Scatter Plots view

Command or option

Description

Options pane

Loads the Option pane settings that you saved with the Save command.

Saves the settings that you selected in the Options pane.

 

Resets the settings of the options in the Options pane to the defaults that were in effect when you installed the application.

Chart Options

Horizontal Grid Lines

Determines whether the scatter plot displays horizontal grid lines and specifies the style of these lines.

  • None: Displays no horizontal grid lines on the scatter plot.
  • (Default) Coarse: Displays horizontal grid lines on the scatter plot that are heavier and farther apart.
  • Fine: Displays horizontal grid lines on the scatter plot that are finer and closer together.

Vertical Grid Lines

Determines whether the scatter plot displays vertical grid lines and specifies the style of these lines.

  • None: Displays no vertical grid lines on the scatter plot.
  • (Default) Coarse: Displays vertical grid lines on the scatter plot that are heavier and farther apart.
  • Fine: Displays vertical grid lines on the scatter plot that are finer and progressively closer together.

Axis Options

X-Axis Title

Specifies the label for the x axis. By default, this option uses the category selected from the X Data list as the x axis title.

X Axis Type

Specifies the axis type (scale) of the x axis.

  • (Default) Linear: Plots the data on a linear scale.
  • Log: Plots the data on a logarithmic scale.

Y-Axis Title

Specifies the label for the y axis. By default, this option uses the category selected from the Y Data list as the y-axis title.

Y Axis Type

Specifies the axis type (scale) of the y axis.

  • (Default) Linear: Plots the data on a linear scale.
  • Log: Plots the data on a logarithmic scale.

Z Axis Type

Specifies the axis type (scale) of the z axis.

  • (Default) Linear: Plots the data on a linear scale.
  • Log: Plots the data on a logarithmic scale.

Axis Title Font

Opens the Font dialog box so that you can specify the font used to denote the axis labels. For information, see the Font dialog box in the Proteome Discoverer Help.

Default: 24-point Arial

Select the arrow next to the Axis Label Font option to display aspects of the label font that you can change, which are as follows:

  • Name: Specifies the label font; default: Arial
  • Size: Specifies the size of the label font; default: 24
  • Unit: Specifies the unit for measuring the size of the label font; default: Point
  • Bold: Specifies the weight of the label font.
    - True: Displays labels in bold font.
    - (Default) False: Displays labels in normal font.
  • GdiCharSet: Specifies a byte value that indicates the GDI character set to use with the selected font; default: 1
  • GdiVerticalFont: Gets a Boolean value that indicates whether the selected font is derived from a GDI vertical font.
    - True: Indicates that the selected font is derived from a GDI vertical font.
    - (Default) False: Indicates that the selected font is not derived from a GDI vertical font.
  • Italic: Specifies whether to italicize the selected font.
    - True: Italicizes the selected font.
    - (Default) False: Does not italicize the selected font.
  • Strikeout: Specifies whether to display the selected font shown with strikeout lines through it.
    - True: Displays the selected font with strikeout lines through it.
    - (Default) False: Does not display the selected font with strikeout lines through it.
  • Underline: Specifies whether to underline the selected font.
    - True: Underlines the selected font.
    - (Default) False: Does not underline the selected font.

Axis Scale Font

Opens the Font dialog box so that you can specify the font used to denote the scale of the x and y axes. For information, see the Font dialog box in the Proteome Discoverer Help.

Default: 18-point Arial.

Select the arrow next to the Axis Scale Font option to display aspects of the label font that you can change, which are as follows:

  • Name: Specifies the label font; default: Arial
  • Size: Specifies the size of the label font; default: 18
  • Unit: Specifies the unit for measuring the size of the label font; default: Point
  • Bold: Specifies the weight of the label font.
    - True: Displays labels in bold font.
    - (Default) False: Displays labels in normal font.
  • GdiCharSet: Specifies a byte value that indicates the GDI character set to use with the selected font; default: 1
  • GdiVerticalFont: Gets a Boolean value that indicates whether the selected font is derived from a GDI vertical font.
    - True: Indicates that the selected font is derived from a GDI vertical font.
    - (Default) False: Indicates that the selected font is not derived from a GDI vertical font.
  • Italic: Specifies whether to italicize the selected font.
    - True: Italicizes the selected font.
    - (Default) False: Does not italicize the selected font.
  • Strikeout: Specifies whether to display the selected font shown with strikeout lines through it.
    - True: Displays the selected font with strikeout lines through it.
    - (Default) False: Does not display the selected font with strikeout lines through it.
  • Underline: Specifies whether to underline the selected font.
    - True: Underlines the selected font.
    - (Default) False: Does not underline the selected font.

Series Options

Points

Specifies the appearance of the items in the scatter plot that pass the used display filters.

To display aspects of the points that you can change, select the arrow next to the Points option. The possible values are as follows:

  • Show Points: Determines whether symbols represent the points in the plot.
    - (Default) True: Symbols represent the points in the plot.
    - False: Symbols do not represent the points in the plot, so the points are not visible.
  • Symbol: Specifies the symbol to represent the points in the plot.
    - Square: Displays the points as squares.
    - Diamond: Displays the points as diamonds.
    - Triangle: Displays the points as triangles.
    - (Default) Circle: Displays the points as circles.
    - XCross: Displays the points as X-shaped crosses.
    - Plus: Displays the points as plus signs.
    - Star: Displays the points as stars.
    - TriangleDown: Displays the points as inverted triangles.
    - HDash: Displays the points as horizontal dashes.
    - VDash: Displays the points as vertical dashes.
  • Size: Specifies the size of the symbols that represent the points; default: 6
  • Fore Color: Specifies the outline color of the symbols that represent the points; default: RoyalBlue
  • Back Color: Specifies the fill color of the symbols that represent the points; default: LightSkyBlue
  • Transparency: Specifies the opacity of the points to signify intensity; default: 0

Checked Points

Specifies the appearance of the items in the scatter plot that you selected in the results report.

To display aspects of the selected points that you can change, select the arrow next to the Selected Points option. The available values are as follows:

  • Show Points: Determines whether symbols represent the selected points in the plot.
    - (Default) True: Symbols represent the selected points in the plot.
    - False: Symbols do not represent the selected points in the plot, so the points are not visible.
  • Symbol: Specifies the symbol to represent the selected points in the plot.
    - Square: Displays the points as squares.
    - (Default) Diamond: Displays the points as diamonds.
    - Triangle: Displays the points as triangles.
    - Circle: Displays the points as circles.
    - XCross: Displays the points as X-shaped crosses.
    - Plus: Displays the points as plus signs.
    - Star: Displays the points as stars.
    - TriangleDown: Displays the points as inverted triangles.
    - HDash: Displays the points as horizontal dashes.
    - VDash: Displays the points as vertical dashes.
  • Size: Specifies the size of the symbols that represent the selected points; default: 10
  • Fore Color: Specifies the outline color of the symbols that represent the selected points; default: Firebrick
  • Back Color: Specifies the fill color of the symbols that represent the selected points; default: Tomato
  • Transparency: Specifies the opacity of the points to signify intensity; default: 0

Filtered-Out Points

Specifies the appearance of the items in the scatter plot filtered out by the current display filter.

To display aspects of the selected points that you can change, select the arrow next to the Selected Points option. The available values are as follows:

  • Show Points: Determines whether symbols represent the selected points in the plot.
    - (Default) True: Symbols represent the selected points in the plot.
    - False: Symbols do not represent the selected points in the plot, so the points are not visible.
  • Symbol: Specifies the symbol to represent the selected points in the plot.
    - Square: Displays the points as squares.
    - Diamond: Displays the points as diamonds.
    - (Default) Triangle: Displays the points as triangles.
    - Circle: Displays the points as circles.
    - XCross: Displays the points as X-shaped crosses.
    - Plus: Displays the points as plus signs.
    - Star: Displays the points as stars.
    - TriangleDown: Displays the points as inverted triangles.
    - HDash: Displays the points as horizontal dashes.
    - VDash: Displays the points as vertical dashes.
  • Size: Specifies the size of the symbols that represent the selected points; default: 6
  • Fore Color: Specifies the outline color of the symbols that represent the selected points; default: Gray
  • Back Color: Specifies the fill color of the symbols that represent the selected points; default: Silver
  • Transparency: Specifies the opacity of the points to signify intensity; default: 0

Excluded Points

Specifies the appearance items in the scatter plot that were excluded in the consensus workflow.

To display aspects of the excluded points that you can change, select the arrow next to the Excluded Points option. The available values are as follows:

  • Show Points: Determines whether symbols represent the filtered-out points in the plot.
    - True: Symbols represent the filtered-out points in the plot.
    - (Default) False: Symbols do not represent the filtered-out points in the plot, so the points are not visible.
  • Symbol: Specifies the symbol to represent the filtered-out points in the plot.
    - Square: Displays the points as squares.
    - Diamond: Displays the points as diamonds.
    - Triangle: Displays the points as triangles.
    - Circle: Displays the points as circles.
    - (Default) XCross: Displays the points as X-shaped crosses.
    - Plus: Displays the points as plus signs.
    - Star: Displays the points as stars.
    - TriangleDown: Displays the points as inverted triangles.
    - HDash: Displays the points as horizontal dashes.
    - VDash: Displays the points as vertical dashes.
  • Size: Specifies the size of the symbols that represent the filtered-out points; default: 3
  • Fore Color: Specifies the outline color of the symbols that represent the filtered-out points; default: LightGray
  • Back Color: Specifies the fill color of the symbols that represent the filtered-out points; default: LightGray
  • Transparency: Specifies the opacity of the points to signify intensity; default: 0

Data Source

Displays the result category to plot the data from. The categories are as follows: Protein Groups, All Proteins, Peptide Groups, PSMs, or MS/MS Spectrum Info.

X Data

Specifies the x-axis data set.

Y Data

Specifies the y-axis data set. You can select the same types of data as for the x-axis data set.

Z Data

Specifies the z-axis data set. You can select the same types of data as for the x-axis data set.