In an S plot, the application sorts a single data dimension and plots it against its index. To draw an S plot, select the index data source for the x axis. The index has the same name as the data item name under consideration (PSMs, Proteins, and so forth), followed by the word Index, for example, PSMs Index.

Procedure

  1. In an open result file, select View > Distribution Charts or select Distribution Charts .
  2. Select the Scatter Plots tab in the Report Item Distribution chart.
  3. From the Data Source list, select the types of data to display.
  4. In the X Data list, select the data set to display on the x axis.
  5. For an S plot, select data_set Index.
  6. In the Y Data list, select the data set to display on the y axis.
  7. Select Refresh.

See the following figure for an example of an S plot.

S-plot

Task

Procedure

Return the settings to the original default settings

In the Options pane, select Factory Defaults.

Zoom in

Drag the cursor to select the area that you want to enlarge.

Zoom out

Drag the cursor to the left and select the area that you want to reduce, or right-click the plot and select Zoom Out.

Return to the default view

Right-click the plot and select Undo All Zoom/Pan.

Select all the visible data points in the scatter plot

Procedure

  1. Zoom in to restrict the view to the area of interest, for example, protein groups with significant up- or down-regulation.
  2. Right-click the chart and select Select All Visible Points.
  3. The application places a check mark in the results file for all the result items—protein groups, proteins, peptide groups, PSMs, and precursor ions—corresponding to the selected data points in the chart. However, you must refresh the screen to see the check marks.
  4. Conversely, you can select the checkboxes for the items in the results file that you want to display in a scatter plot.

Clear the visible data points in the scatter plot

Right-click the plot and select Deselect All Visible Points.

Select a single data point in the scatter plot

Right-click the data point in the scatter plot and select Select Point.

Deselect a single data point in the scatter plot

Right-click the data point in the scatter plot and select Deselect Point.

Copy a scatter plot image

Procedure

  1. Right-click within the image pane, and select Copy > Image.
  2. The application copies the image to the clipboard.
  3. In another application, paste the contents of the clipboard.

Copy the points in a scatter plot as text

Procedure

  1. Right-click within the image pane, and select Copy > Data.
  2. The application copies the data to the clipboard.
  3. In another application, paste the contents of the clipboard.
  4. The contents appear as text in the document.

Save a scatter plot as an image file

Procedure

  1. Right-click within the image pane, and select Export > Image As.
  2. In the Save As dialog box, locate the folder where you want to save the file, select the file type, and enter the file name.
  3. Select Save.
  4. The application creates a file containing the image.

Save the data from the scatter plot in a text file

Procedure

  1. Right-click within the image pane, and select Export > Data As.
  2. In the Save As dialog box, locate the folder where you want to save the file and enter the file name.
  3. Select Save.
  4. The application creates up to four text files depending up your settings.