A histogram plots grouped numerical data as a column chart. The data groups are usually defined by a given range of data, and the count of the data values in this range is used as the y-axis value to define the column height. You can display the data as a column chart, a bar chart, or two types of line chart.

The numerical data categories of the open results report that are available for the histograms are listed in the Data Source selection box at the top of the Report Item Distribution dialog box.

The Options pane lists the different options that you can use to customize the histogram. For detailed information on these options, refer to Parameters on the Histogram view in the Proteome Discoverer Help. Key options are binning options that define how the data groups are created, options for defining and displaying decoy data, an option that controls excluded items, and an option that displays only items marked by a check mark in the results report. Pointing to the columns activates a tooltip with information about the data category.

Procedure

  1. Select View > Distribution Charts, or select Distribution Charts .
  2. Select the Histograms tab in the Report Item Distribution dialog box.
  3. From the Data Source list, select the type of data to display as a histogram, and then select Refresh.
  4. (Optional) Hide the Options pane by selecting Auto Hide .
  5. The vertical icon shows the pane; the horizontal icon hides the pane. Point to Options to access the hidden pane.
  6. Use the options in the Options pane to adjust the colors, labels, and legends of the display. Refer to Parameters on the Histogram view in the Proteome Discoverer Help.
  7. –or–
  8. In the Options pane of the Report Item Distribution chart, select Load to load the settings that you most recently saved.
  9. See the following figure for an example of a histogram with columns that plot the PSM XCorr scores. The dark red and black bars represent the report target and decoy PSMs. The light red and gray bars show the target and decoy PSMs that were excluded in the report processing. The tooltip shows details of the data group.
  10. Histogram with columns
  11. The following figure shows the same data as a histogram with lines.
  12. Histogram with lines
  13. To compare distributions, you can use a cumulative histogram. For these charts, the application calculates the column height as the height of the current column plus the sum of all previous columns. The rightmost column height is therefore the total log, linear, or percentage, depending on the y-axis settings. The plot is best shown as lines or as step lines, which you can select with the Chart Type option. A Gaussian distribution displays an S-shaped graph. Comparing two Gaussian distributions is often easier in a cumulative chart.
  14. For example, the following figure shows the distribution of the XCorr value for target peptides in red and decoy peptides in black. (These are unfiltered results, so the values are low.) The slower ascension of the red curve points to more confident target hits.
  15. Cumulative histogram in line format
  16. (Optional) To save all the settings that you have chosen, select Save in the Options pane.
  17. The new settings overwrite any previously saved settings. The application loads these new settings when you select Load.
  18. Do any of the tasks listed in the following table.

Task

Procedure

Return the settings to the original default settings

In the Options pane of the Report Item Distribution chart, select Factory Defaults.

Copy a histogram image

Procedure

  1. Right-click 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 histogram as text

Procedure

  1. Right-click the image pane, and select Copy > Data.
  2. The application copies the image to the clipboard.
  3. In another application, paste the points in the chart.

Save a histogram as an image file

Procedure

  1. Right-click 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 histogram in a text file

Procedure

  1. Right-click 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 a file that contains the data range describing the histogram column and the count values for the target, decoy, and excluded items, if they are selected.

Close the Report Item Distribution chart

Procedure

  1. Select Report Item Distribution icon or the "x" in the upper-right corner.
  2. The application stores the chart settings that you selected. When you reopen the chart, it displays these stored settings if they are available.