Adding new tracks to pyGenomeTracks only requires adding a new class to the pygenometracks/tracks folder. The name of the file must end with Track.py. The class must inherit the GenomeTrack (or other track class available) and must have a plot method. In order to work well with the config checker it should also have some global variable: - DEFAULTS_PROPERTIES is a dictionary where each key is a parameter and each value is the default value when it is not set or when something goes wrong. - NECESSARY_PROPERTIES is an array with all the parameters which are necessary for this track (usually 'file') - SYNONYMOUS_PROPERTIES is a dictionary where each key is a parameter, each value is a dictionnary where each key is a string that should be replaced by the value (for example, SYNONYMOUS_PROPERTIES = {'max_value': {'auto': None}}) - POSSIBLE_PROPERTIES is a dictionary where each key is a parameter, each value is an array with the only possible values for this parameter, if the value specified by the user is not part of them, it will be substituted by the default value. - BOOLEAN_PROPERTIES is an array with all parameters that should have a boolean value (a boolean value can be 0, 1, true, false, on, off) - STRING_PROPERTIES is an array with all parameters that have string values. It should always contains title and file_type. - FLOAT_PROPERTIES is a dictionnary where each key is a parameter, each value is an array with the min value (included) and the max value (included) that should have the parameter (You can use [- np.inf, np.inf] if there is no restriction). This dictionary should always contains 'height': [0, np.inf] - INTEGER_PROPERTIES same as FLOAT_PROPERTIES for integer values.
Additionally, some basic description should be added.
For example, to make a track that prints 'hello world' at a given location looks like this:
../../examples/helloWorldTrack.py
The OPTIONS_TXT should contain the text to build a default configuration file. This information, together with the information about SUPPORTED_ENDINGS is used by the program make_tracks_file to create a default configuration file based on the endings of the files given.
The configuration file is:
../../examples/new_track.ini
$ pyGenomeTracks --tracks new_track.ini --region X:3000000-3200000 -o new_track.png
Notice that the resulting track already includes a y-axis (to the left) and a label to the right. Those are the defaults that can be changed by adding a plot_y_axis and plot_label methods.
Another more complex example is the plotting of multiple bedgraph data as matrices. The output of HiCExplorer hicFindTADs produces a file whose data format is similar to a bedgraph but with more value columns. We call this a bedgraph matrix. The following track plot this bedgraph matrix:
../../examples/BedMatrixExampleTrack.py
Let's create a track for this:
../../examples/bedgraph_matrix.ini
$ pyGenomeTracks --tracks bedgraph_matrix.ini --region X:2000000-3500000 -o bedgraph_matrix.png
Although this image looks interesting another way to plot the data is a overlapping lines with the mean value highlighted. Using the bedgraph version of pyGenomeTracks the following image can be obtained:
