ProtPlot Menus

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Menu Descriptions for ProtPlot

The user interacts with ProtPlot via various direct manipulation controls including:

These controls are shown in the following figure:

Interrogating the database by clicking on a spot in the scatterplot

You may interrogate the database by clicking on a spot in the scatter plot. This will report data for that protein in the upper right part of the scatterplot window. The actual data reported depends on which display mode you have selected. All entries show the SP-ACC and SP-ID. Additional data is added depending on the display mode:

Mw and pI upper and lower limits sliders

The upper and lower limits of Mw and pI may be controlled directly thorugh sliders on the left and right respectively as shown in the following figure.

The continuous parameter threshold slider controls

Parameters may be defined interactively using direct manipulation sliders on the right side of the main window. These right slider controls include:

Samples menu and checkboxes in the lower command bar

These lower controls include:

Pull-down menu commands in the upper menu bar

The top pull-down menu selections include commands which invoke an action, checkbox options [CB] which are independent of one another, and radio button options [RB] which may only have one member active at a time. Menu entries followed by the Indicates the menu entry has a submenu symbol, indicate that the menu entry has a submenu. Selections prefaced with a '' and indicate '' indicate that the command is a checkbox that is enabled and disabled respectively. Checkbox menu items have a "[CB]" at the end of the command. Selections prefaced with a '' and indicate '' indicate that the command is a multiple choice "radio button" that is enabled and disabled respectively, and that only one member of the group is allowed to be on at a time. Radio button menu items have a "[RB]" at the end of the command.

There are a number of pull-down menus in ProtPlot including:

  1. File - select samples, save the state and quit
  2. View - select viewing options
  3. Genomic-DBs - enable access to popup Web genomic databases
  4. Filter - select protein data filter options
  5. Plot - select primary plot mode and plotting options
  6. Cluster - select cluster distance metrics and perform clustering
  7. Report - generate popup reports
  8. Help - the help menu - local and server based

File menu

This provides commands to select samples for the
current, X, Y, X- and Y-sets, and EP-set of samples. It invokes a popup sample chooser. Find a protein by SwissProt Accession number (SP-ACC) or SwissProt ID (SP-ID). Save and restore the data-mining state. Update ProtPlot and its data from the Web server.

View menu

Specify various scatterplot viewing options.

Genomic-DBs menu

This connects ProtPlot with various Genomic databases. If enabled, it will pop up a Web browser for the selected protein on the specified Genomic database.

Filter menu

Select the data filter options. If you change an option or adjust a parameter slider, it will re-run the data filter. See
table of filters as a function of display mode.

Plot menu

Specify the scatterplot display. Switching from expression data to ratio data changes the expression range sliders to ratio range sliders (and vice-versa). The Expression Profile plot is enabled from this menu. See
table of filters for a discussion on display modes.

Cluster menu

Initiate clustering. Specify the distance metric. When clustering is enabled, the Cluster Distance Slider (D) is active. After you have defined an initial cluster, you may popup up a scrollable list of EP plots for the clustered proteins. These are sorted by the similarity order in the
cluster report

Report menu

Generate various tab-delimited reports that may be saved or cut-and-pasted into MS Excel. See
table of reports as a function of display mode.

Help menu

Help is available on the Web site and make be invoked from ProtPlot when it is running by selecting a topic.


Djamel Medjahed, LMT, SAIC-Frederick
Peter Lemkin, LECB, NCI-Frederick

Revised: 08-26-2004