Graphics export
CLC Genomics Workbench supports two ways of exporting graphics:
- You can export the current view, either the visible area or the entire view, by clicking on the Graphics button (
) in the top Toolbar. This is the generally recommended route for exporting graphics for individual data elements, and is described in Export graphics to files.
- For some data types, graphics export tools are available from the main Export menu, which can be opened by clicking on the Export (
) button in the top Toolbar. These are useful if you wish to export different data using the same view in an automated fashion, for example by running the export tool in batch mode or in a workflow context. This functionality is described below.
Using export tools to export graphics
The following types of data can be exported using dedicated export tools:
- Alignments
- Fusion plots from fusion gene tracks
- Heat maps
- Read mappings
- Sequences
- Tracks
- Track lists
If exporting fusion plots, please refer to the notes at the end of this section for details specific to that exporter.
The general actions taken are:
- Click on the Export () button in the top Toolbar or choose the Export option under the File menu.
- Type "graphics" in the top field to see just a list of graphics exporters, and then select the one you wish to use. For example, if you wish to export an alignment as graphics, select "Alignment graphics" in the list.
- Select the data elements to be exported.
- Configure any relevant options. Detailed descriptions of these are provided below.
- Select where the data should be exported to.
Options available when exporting sequences, alignments and read mappings to graphics format files are shown in figure 8.16.
Figure 8.18: Options available when exporting sequences, alignments and read mappings to graphics format files.
Options available when exporting tracks and track lists to graphics format files are shown in figure 8.17. Additional notes relating to output naming when exporting fusion plots from a fusion gene track are provided at the end of this section.
Figure 8.16: Options available when exporting tracks and track lists to graphics format files.
The format and size of the exported graphics can be configured using:
- Graphics format: Several export formats are available, including bitmap formats (such as .png, .jpg) and vector graphics (.svg, .ps, .eps).
- Width and height: The desired width and height of the exported image. This can be specified in centimeters or inches.
- Resolution: When exporting to bitmap formats (JPG, PDF, PNG, TIF), this setting defines the pixel width and height to use for the exported image. This value is not used when exporting to vector based formats (SVG, PS, EPS). Exported files do not contain a DPI metadata value. Downstream graphics software may enter a default value when the image is opened.
The appearance of the exported graphics can be configured using:
- View settings: The view settings available for the data type being exported. To determine how the data will look when a particular view is used, open a data element of the type you wish to export, click on the Save View button visible at the bottom of the Side Panel, and apply the view settings in the dialog that appears. View settings are described in Side Panel view settings. Custom view settings will be available to choose from when exporting if the "Save for all <data type> views" option was checked when the view was saved.
- Region restriction: The region to be exported. For sequences, alignments and read mappings, the region is specified using start and end coordinates. For tracks and track lists, you provide an annotation track, where the region corresponding to the full span of the first annotation is exported. The rest of the annotations in the track have no effect.
Notes about exporting fusion plots from fusion gene tracks
When configuring the export of graphics from fusion gene tracks, it is highly recommended that the {name} placeholder is used in the Custom file name setting.
Each fusion plot from a fusion gene track is exported as an individual file. By default, they are bundled in a zip file. Using the {name} placeholder has the following effects:
- The name of the input track or report is included in the name of the zip file.
- The fusion name is included in the name of the file containing the corresponding fusion plot.
To see the individual file names that will be used, choose the gzip or None option in the Use compression drop-down list, and hover the cursor over the Output file name field (figure 8.18). Then select zip again if you wish the files to be bundled into a zip fie.
Figure 8.17: The fusion plots from a fusion gene track are being exported. The option "None" has been selected for "Use compression", so the tool tip over the "Output file name" field contains the names of the individual files that will be created. The {name} placeholder is included in the "Custom file name" field, so those file names contain the fusion names.