A scatter plot shows the distribution of data as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. A scatter plot is useful when you are trying to refine your methods or to determine whether a mass spectrometer is properly calibrated. You can select or clear all points that are currently visible in the chart, or you can select or clear single points.
You can plot four data series in a scatter plot:
- Items that are not selected in the report and pass the display filters
- Items that are not selected in the report and do not pass the display filters
- Items that are selected in the report whether or not they pass the display filters
- The application displays these items whether or not they are filtered out by the current display filter.
- Items that are not displayed in the report because they were excluded in the consensus workflow
You can also plot the data in a scatter plot called an S plot (see Display an S plot).
Procedure
- In an open result file, select View > Distribution Charts, or select Distribution Charts
. - Select the Scatter Plots tab in the Report Item Distribution chart.
- From the Data Source list, select the types of data to display.
- In the X Data list, select the data set to display on the x axis. To draw an S plot, see Display an S plot.
- In the Y Data list, select the data set to display on the y axis.
- (Optional) In the Z Data list, select the data set to display on the z axis.
- Selecting a data value for the z axis adds a color gradient to the plotted data points ranging from the lowest to the highest Z data value.
- Select Refresh to draw the chart.
- (Optional) Hide the Options pane by selecting Auto Hide
. - The vertical icon shows the pane; the horizontal icon hides the pane. Point to Options to access the hidden Options pane.
- Use the options in the Options pane to adjust the colors, labels, and legends of the display.
- For information on these options, refer to the Parameters on the Scatter Plots view in the Proteome Discoverer Help.
- –or–
- In the Options pane, select Load to load the settings that you most recently saved.
- The following figure shows an example of a scatter plot.
- A scatter plot with this distribution might indicate that you should modify your search workflow to use a ±5 ppm delta mass instead of 15 ppm because all the best peptides fall within the tighter tolerances.
TIP
When you want to indicate the point density, use a darker color for the points and their borders and set the Transparency parameter to a value between 60% and 90%. For a larger number of points, higher transparency values result in better appearance.
- Pointing to a data point in the chart activates a tooltip with information about the underlying result item.
- Double-clicking a data point in the scatter plot selects the corresponding row in the master table.
- The default display shows the properties of all currently visible peptides.
- Tooltip information that describes the identified protein, amino acid sequence, charge state, or other plotted items appears by default.
- (Optional) To switch off the display of the tooltip information, right-click and select Show Position Tooltips.
- (Optional) To save all the settings that you have chosen, select Save in the Options pane.
- The new settings overwrite any previously saved settings. The application loads these new settings when you select Load.
- To close the Report Item Distribution chart, select Report Item Distribution icon or the "x" in the upper-right corner.
- When you close the Report Item Distribution chart, the application stores the chart settings that you selected. When you reopen the chart, it displays these stored settings if they are available.