3.6.3. GenomeBrowse View¶
The GenomeBrowse view contains an instance of GenomeBrowse embedded in VarSeq. Most of the features of GenomeBrowse in VarSeq are the same as in the stand-alone version, however, there are a few differences.
Navigating the GenomeBrowse Window¶
On the GenomeBrowse Window there are several regions to note and become familiar with:
The location and navigation bar features back/forward buttons to retrieve previous zoom locations, a chromosome selector, a genomic location bar, and an external browser link list. Each feature is described below.
Back/Forward buttons: These buttons act similar to Internet browsers, they enable you to jump back to the previous zoom or go forward to the next zoom. A slow click or right-click will bring up a zoom history to jump back or forward to a specific zoom from some point in the immediate history.
Chromosome Selector: This dialog contains a drop down list of chromosome names. The whole genome view can be obtained by selecting All from the list. Also, a chromosome name(s) can be typed in the box to jump to it rather than selecting it from the list. Examples of input include 1, 1-3, etc.
Genomic Location Bar: A chromosome and position string can be entered into this dialog to jump to the region. Cytobands and gene names can also be entered into this dialog. Once the region has been entered, either click on the “Go” or “Play” button, press “Enter”, or select a region from a list of potential zooms when applicable to jump to the desired genomic coordinates.
External Browser Links: Multiple external browsers can be accessed for the zoom region specified in the Genomic Zoom Region box. Regions spanning multiple chromosomes are not supported by the external browsers and will result in a warning when attempting to link out.
There are two zoom modes, navigation pointer mode and zoom mode.
Navigation pointer mode allows for click-and-drag operations in plots or scales to pan the view. Right-click-and-drag operations cause the view to be scaled around the initial click point. The scroll wheel zooms the view in and out. This mode can be accessed using the hot-keys a or p.
Zoom mode allows for click-and-drag selection of a region in plots or scales. When the drag operation is concluded, the selected region will become the new view. Right-click-and-drag selection will zoom the view in such a way that the previous view fits inside the selected region in the new view. In other words, selecting a small region with the right mouse button causes the view to zoom out a lot. Selecting a large region with the right mouse button causes the view to zoom out a little bit. The scroll wheel zooms the view in and out in this mode as well. This mode can be accessed using the hot-key z.
Any drag operation can be canceled by pressing the opposite mouse button during the drag. Cancel a left-drag by pressing the right mouse button. Cancel a right-drag by pressing the left mouse button.
The general toolbar contains controls for adding plots, saving all plots in the view as an image, and setting default options for a GenomeBrowse window.
The genome assembly (species/build) can be changed through the genome selectiong drop down menu on the genome toolbar. Recently used or common genomes are at the top of the list, otherwise all genome assemblies available are listed alphabetically by the scientific name.
The order and visibility of segements in the selected genome assmebly can be changed by selecting the Hide/Show eyeball icon on the genome toolbar. See Managing Genome Assembly Views for more information.
The zoom tool bar offers a zoom slider and buttons for zooming the view in and out only on the x-axis. Slide the bar to the left (toward the minus - button) to zoom out, slide the bar to the right (toward the plus + button) to zoom in. The buttons zoom view in (+) or out (-) on the x-axis in steps.
The domain view provides genome wide context. If a cytoband source for the current genome assembly is available in any “bookmarked” location (See dslLocations for more information) it will be set as the domain view plot by default. Any plot can be set as the domain view plot by right clicking on the source and selecting Set as Domain View Plot. If a cytoband source is available but not currently set as the domain view plot, the option to restore it will be provided in the right-click menu for the domain view plot.
The domain view also includes chromosome labels, the domain view funnel which illustrates the mapping of the current view from the x-axis scale onto the domain view plot, and the current x-axis scale. Each of these components can be hidden or shown by right clicking on the domain view and checking the appropriate entry in the menu.
The main portion of the GenomeBrowse window is the plot view. This is the region of the window where the sources are drawn in plots. Each plot in the plot view has several special features.
Rearrange Plots: Plots in the plot view can be rearranged by clicking, dragging, and dropping the grab bar on the left of the plot.
Controls: Some common plot controls are accessible for many plots by hovering over the upper left corner of the plot and clicking on the gear icon. The complete set of controls is available in the control panel (docked in the middle of the left side of the GenomeBrowse window by default). The control panel acts on the current selection and may be composed of multiple tabs depending on what is selected.
Feature List: The feature list can be shown or updated to include information for the first data source in a plot by hovering over the upper left corner of the plot and clicking on the table icon. The feature list can also be shown or updated to the first data source in the plot by right clicking on the plot and selecting Feature List. Once the feature list is shown, a different data source can be selected by name from the drop-down box in its upper left corner.
Title Editing: The title can be edited in place by double clicking on the plot title. It can also be edited by right clicking on the title and selecting Edit Title…, or through the control panel.
Data Source Location: The location of the data source for the plot is displayed above the upper right corner of plot.
Scale Label Editing: The labels for both the x-axis and y-axis can be modified. When visible, they can be edited in place by double clicking on them. They can also be edited by right clicking and selecting Edit [X/Y]-Axis Label…, or through the control panel.
Y-axis Zoom Mode: The current y-axis zoom mode can be identified by hovering over a plot. The second button from the top in the upper right corner will show a letter designating the current mode. The current y-axis zoom mode can be changed by clicking on that button and choosing one of the available modes from the menu. There are four available y-axis zoom modes:
- Manual - The y-axis zoom is controlled manually and all zoom controls are
enabled. This mode can be accessed using the hot-keys r or m.
- Hold - The y-axis zoom is controlled manually but vertical panning on the
plot canvas is disabled, protecting against accidental changes to the y-axis zoom. All zoom controls are enabled. This mode can be accessed using the hot-keys e or h.
- Fit Data - The y-axis zoom is changed dynamically as the x-axis zoom changes
to show all the data on the vertical axis. All vertical zoom controls are disabled. This mode can be accessed using the hot-keys w or f.
- Auto - The y-axis zoom is changed dynamically as the x-axis zoom changes.
When zooming in close on the x-axis the y-axis will be zoomed in as well to automatically improve the detail of the vertical axis in proportion to the horizontal axis. This mode is only available on Heat Map, Alignment Pile-up, Value, and Variant Map plots. It can be accessed using the hot-key q.
By default the y-axis zoom mode is either Fit Data or Auto depending on whether the plot type supports Auto zoom. If the zoom mode is changed to either Manual or Hold zoom, adjustments to the y-axis will become possible. In particular this will make click-and-drag operations on the y-axis scale function. It will also cause the y-axis zoom slider to appear along the right edge of the plot (assuming the plot is tall enough). The y-axis zoom slider is analogous to the x-axis zoom slider provided by the Zoom tool bar. Drag the slider toward the minus (-) button to zoom out, and toward the plus (+) button to zoom in. The buttons zoom in (+) or out (-) in steps.
Mouse Anchor: A vertical line that is drawn over all plots in the plot view can be set by right clicking on a plot and selecting Place Mouse Anchor or by pressing Ctrl - `. This can be used as a visual reference, a bookmark or a ruler. To jump to the current mouse anchor press ` (also the tilde key). To clear the current mouse anchor right click and select Clear Mouse Anchor or press Alt - `. When a mouse anchor is set, the distance between it and the current mouse pointer location will be displayed in the status bar. Note that the precision of the measurement is dependent on the current zoom.
Searchable: The data sources for a plot can be set to be searchable by right clicking on the plot and selecting Searchable. This will add the plot’s data sources to the list that gets searched when text is typed into the location bar.
Feature Labels: Feature labels on some plots can be hidden or shown by right clicking on the plot and selecting the Feature Labels in the Show menu.
Reload: A plot can be reloaded by right clicking and selecting Reload.
Hide: A plot can be hidden by hovering over the upper right corner of a plot and clicking on the minimize icon, or by right clicking on a plot and selecting Hide. To restore a hidden plot re-check it in the plot tree or right-click on empty space in the plot view and re-check its entry in the Show Plot/Group menu.
Delete: A plot can be deleted by selecting it in the plot view and pressing the delete button on a keyboard or right clicking on the plot and selecting Delete from the menu.
Plot: Plots can be added by right clicking on empty space in the plot view (anywhere that is not a plot) and selecting Plot. Additional items can be added to value plots by right clicking on the plot and selecting Add Plot Item(s).
Resize Plots: A plot can be resized by clicking on the grab bar underneath it and dragging up or down to the desired size. Plots have a minimum height but there is practically no maximum.
Contains the controls for the selected plot, plot group, or plot item. See the specific plot type for information on the available controls. (GenomeBrowse Options for Specific Plot Types)
Displays information about plots and their data. Clicking on a plot, a node in the plot tree, or a feature within a plot will update the information in the console. Please see the specific plot type for descriptions of the information that can be displayed in the console.
Checking the History check box will cause information for multiple recent clicks to be accumulated in the console by inserting the most recent information at the top. Clicking the Clear button will empty all information from the console.
The feature list is a tabular view of all data fields available for each feature in a data source. Up to 1000 features can be read at a time, and can be read from either the start of the genome assembly, or the current zoom.
A different data source available from the current GenomeBrowse window can be selected from the drop-down list in the upper left corner of the feature list. This will cause the table to be re-populated with features from the selected source.
Selecting the All radio button will update the feature list with features from the start of the genome assembly. Selecting the Zoom radio button will update the feature list with features from the current x-axis zoom. Selecting one or more features in the list will zoom the view to fit the selected feature(s).
The list of features can be sorted by clicking on the field names (column headers). Once for ascending order, twice for descending order.
Selected row(s) can be copied to the clipboard. Click on a row or use Ctrl+left-click or Ctrl-A to select multiple or all rows. Then right-click and select Copy Selected Row(s) to Clipboard or Copy Selected Row(s) with Headers. This table can then be pasted into a spreadsheet program or text file.
The mouse anchor can be set to the center of any feature in the table by right clicking on its row and selecting Place Mouse-Anchor At …
If there are more than 1000 features available, the read more link will be shown in the lower left corner. Up to 1000 more features will be added to the table each time it is clicked.
General Options for GenomeBrowse¶
The options dialog contains various controls for setting global GenomeBrowse options. These options will apply to all GenomeBrowse windows in all projects. Available controls include a choice for where new plots are added to the plot view, which axes position tracking is enabled on, download save target, and color customization.
Saving Plots from a GenomeBrowse Window¶
Plots can be exported to several image formats.
When saving a plot, only non-hidden graphs in the GenomeBrowse window will appear in the output along with the optional currently visible Domain View plot.
Saving GenomeBrowse Plots to Image Formats¶
To save all visible plots to an image file, select File > Save As Image. This opens the Save As Image dialog which includes a preview of the image that will be saved as well as various options applicable to saving an image.
Image Size: The current size of the plot window in pixels is displayed. The size is dependent on the original size of the GenomeBrowse window. To change the image size adjust the original GenomeBrowse window before launching the Save As Image dialog.
Preview of Image: A scaled view of the image to be saved is displayed in the dialog. Larger plots may take longer to draw, if the image has not finished drawing before Save is pressed an additional progress dialog will appear. Once the rendering of the image has finished the image will be saved.
Domain View: The domain view plot is shown at the top of the image. This view can be shown by checking this box.
Margins: The top, bottom, left and right margins (in pixels) can be altered independently. Click the Unlock button to the right of the current selections and adjust the appropriate control box.
To save the image click Save. To cancel and return to the GenomeBrowse window, click Cancel. If an output file has not been selected, a reminder to choose an output file before proceeding will appear.