The FeatureEmitter processing module generates a denovo grid of features on the genome. It is primarily used along with TemplateCluster to create regular gridded histogram-like expression on a genome. It can output features on the region of query or the whole genome. The output are simple features with coordinates, and a name. The granularity of the grid is controlled using either the num_per_region or the width parameter
- <dynamic/> : specify that the width of generated grid of features is dynamically calculated based on the genomic region queried and the display_width of the visualization. This is the default behaviour.
- <width> : specify the desired width of the grid of features. for a specified region query, it will generate this many total features and adjust the feature sizes accordingly. If <width> is specified, the dynamic behaviour is disabled and features will always be generated at this width.
- <fixed_grid> : for a region query, realign the start so that it falls on a regular grid which are integer multiples of the feature width. values are true/false
- <both_strands> : defines if the grid of features should be generated on both strands (two for each location) or if it will generate strandless features. values are true/false
- <coarseness> : for dynamic width grid, defines the level of coarseness of grid-feature to pixel mapping. ex coarseness of 3 means grid-element will map to 3 pixels in the visualization.
The expression binning GUI provides for a convenient graphical interface to display data as a wiggle plot / fixed-grid-binned histogram.
Often after a chain of processings, it is desirable to display the data in a similar fashion.
Below is an example of the section to be added as the final step of the processing chain to attain the same results as the expression binning GUI with parameters "overlap mode:area"; "expression binning:sum"; "process ignoring strand:unchecked"; "overlap via subfeatures:checked" .
... your spstream modules chain here ...
<spstream module="TemplateCluster"> <overlap_subfeatures>true</overlap_subfeatures> <side_stream> <spstream module="FeatureEmitter"> <dynamic/> <fixed_grid>true</fixed_grid> <both_strands>true</both_strands> </spstream> </side_stream> </spstream>
This script combines a FeatureEmitter with TemplateCluster to create a regular grid of features at a 100base resolution and collates expression evenly into each overlapping "bin".
<zenbu_script> <stream_processing> <spstream module="TemplateCluster"> <overlap_mode>height</overlap_mode> <expression_mode>sum</expression_mode> <overlap_subfeatures>true</overlap_subfeatures> <ignore_strand>true</ignore_strand> <side_stream> <spstream module="FeatureEmitter"> <width>100</width> <fixed_grid>true</fixed_grid> <both_strands>false</both_strands> </spstream> </side_stream> </spstream> </stream_processing> </zenbu_script>
Example ZENBU view showing this script in use