FreeView is a gene expression dendrogram viewer. It allows easy viewing of gene expression dendrograms and zooming in on details in them using a variety of color and visualization schemes that can easily be created. Saving images of dendrograms is also a very powerful feature.
FreeOView is a gene expression visual optimizer and dendrogram viewer. It allows everything FreeView does. Its additional features compared to FreeView are manual optimization using a fitness indicator and algorithmical optimization using a variety of optimization methods and measures of dendrogram optimality. Comparing optimized dendrograms with the original is designed to be as easy as possible.
The main window of both FreeView and FreeOView consist of three parts, the menus, the main part of the window and the status bar. The status bar displays currently selected subtree and its similarity valued on the left, current file on the right. The status bar of FreeOView also displays the current fitness in the middle. Main parts of both windows are exactly the same except for the fact that FreeOView can display two dendrograms one above the other. The main part of the window is vertically divided into to parts. The left one contains the dendrogram. When a part of the dendrogram is selected, the right one contains zoomed part of dendrogram with gene descriptions. You can select a part of the dendrogram in three ways. You can click on or right of a node (but left of any of its sub nodes on the right) to select the part of the dendrogram starting with that node. Dragging the mouse over gene expressions selects the smallest subtree containing both the gene from which you started dragging the mouse to where you dragged the mouse to. The third way of selecting genes is with the keyboard, but only if a part of dendrogram is already selected. The left arrow selects the supernode of the currently selected node, the up and down arrow select the upper or lower subnode of the currently selected node, and the right arrow selects the supernode, if the value of similarity is bigger than the cutoff value, which can be set in the options dialog.
The menus of Free(O)View consist of:
Loads dendrogram data from a selected .cdt file and .gtr file with the same name and displays it.
Saves dendrogram data to the same files.
Inverts the selected subtree of the tree (exchanges its subtrees)
Mirrors the selected subtree (turns it upside-down).
Find gene dialog allows you to search for certain genes within the dendrogram. Type the name or starting part of a name of a gene to look for in the edit box provided. Press on the Find button to start searching. Press on the Find Next button to search for next occurrence of the gene. If a gene is found it is selected in the dendrogram and zoomed on.
Save image dialog allows you to save dendrogram images or part of them in various formats. You can select which part of dendrogram you want to save in the image and whether or not to save the whole image or only the selected part of it. You can also select in which image format you want the saved image to be. After pressing the save... button you are taken to the file selection dialog, when you can select a name for your saved image.
The options dialog is divided in three parts. The left side is used for selecting options. It is organized in three tabs for selecting different types of options: sizes, colors and other. On the top right are scheme managing controls, consisting of a combo box for selecting a scheme and buttons for saving and deleting schemes. On the bottom right there is a preview pane where a small dendrogram is shown using the currently selected scheme. On the bottom there is a row of buttons for closing the dialog box with or without accepting the options, for resetting options and for displaying this help.
The optimization dialog is divide in three parts. On top you can select there are two tabs, one for selection optimization function and the other for selecting optimization method. When a certain function or method is selected using the combo boxes, its options can be set below. The middle part of the dialog is used for optimization itself. On top of this part is the current value of the optimization function (fitness). Below that are two progress bars. The left one shows progress in the current step or generation of optimization, the right one shows progress of the optimization in general. The lowest part of the dialog is a row of buttons for closing the window, resetting the options and displaying this help.