Help: The User Interface
- Starting Up
- The User Interface
- Analyzing gene expression regulation data
- Using the Bucket, working with pathways
- Searching for genes and pathways
- Uninstallation
- Known Issues and Bugs
Selecting Elements
Caleydo knows two types of selections: mouse-over and clicked. Mouse-over highlights an element in all visualizations by either framing or drawing it in yellow. Mouse-over selections are fast but volatile. That means, that it is easy to accidently select something. A more persistent selection is the clicked selection. A clicked element is shown in violet.
When you right-click any element, you get an context menu with available options for that item.
GUI Overview
The
GUI of Caleydo consist of three main parts: The menu bar on the top, the
side bar containing tool bars, information and settings and the main
area, where the different visualizations are rendered.
Caleydo is optimized for the use with widescreen monitors. If you
use a traditional 4:3 monitor the side bar will be placed in between the
main area and the menu bar, instead of on the side.
The Menu Bar
The
menu bar provides access to file operations, such as loading and
exporting of data, to a search tool etc. The most important part of the
menu bar is the View drop-down, which allows you to open the
different views that come with Caleydo.
The File drop-down allows you to load and export data, as well as open the preferences.
The Help allows you to view the log generated by Caleydo,
provides access to a database with known bugs, where you can also report
a new bug and links to this help pages.
Side Bar
The
side bar consists of three parts: The tool bar, where all the control
buttons and elements are placed, an info area, where information about
the current selection is displayed and the color mapping which allows
you to view and modify the color mapping for your data.
The tool bar changes depending on the visible views. For example, if you close the one view, the associated tool bar disappears. Also, the tool bar associated with a view which is currently active is highlighted.
The info area shows information on the currently selected elements. Elements that are selected by just holding the mouse over them are displayed in yellow, elements that are clicked are displayed in violet.
Since a single entry in the data is associated with two attributes (row and column, gene and experiment for the genetic use case) both are shown.
The color
mapping view displays how color is mapped to the loaded data. You see a
histogram, which shows you the distribution of the values. By dragging
the blue bars, the color mapped to a value can be adjusted. Between the
bars, the color is interpolated, within the bars, the color is constant.
Consequently you could create a large constant area by dragging the
outer two lines of the central bars to the left resp. the right.
Below the histogram the three values corresponding to the central line of the bars is shown. Notice, that scientific notation is used when values are to large. This example uses a logarithmic scale, which is evident when looking at the values.
By double-clicking at the bar between the histogram and the values, the preference page for the color mapping opens, where you can adjust the colors. This is also accessible via File > Preferences
Since correctly adjusting the color mapping is important for gene expression analysis, you can also drag the color mapping to the main area, where you can fine-tune the mapping.
Main Area
All views are placed in the main area of Caleydo. When you click View and pick a view in the menu bar it is opened into the main area. To switch between views, you can use the tab bar on top of the views, to close views, click the X on the tab (which is only visible when the view is visible).
A crucial feature for a multiple view visualization system is the arbitrary arrangement of windows. Caleydo allows you to drag a view to nearly every position imaginable. An example is show in the screen-shot, where two views are placed side by side, one view is placed at the bottom, and one view is dragged onto a second screen, independent of the main application window.
When you place a view outside of the main window, it also takes its tool bar with it. The tool bar is placed on the top right corner of the view.
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website maintained by Marc
Streit and Alexander
Lex
last updated on 2010-07-29