change file_type x-axis to x_axis (#233)

docs/content/all_default_properties_rst.txt

@@ -1,5 +1,5 @@
 =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================
-parameter                  :doc:`tracks/x-axis`       :doc:`tracks/epilogos`     :doc:`tracks/links`        :doc:`tracks/domains`      :doc:`tracks/bed`          :doc:`tracks/gtf`          :doc:`tracks/narrow_peak`  :doc:`tracks/bigwig`       :doc:`tracks/bedgraph`     :doc:`tracks/bedgraph_mat  :doc:`tracks/hlines`       :doc:`tracks/hic_matrix`   :doc:`tracks/scalebar`   
+parameter                  :doc:`tracks/x_axis`       :doc:`tracks/epilogos`     :doc:`tracks/links`        :doc:`tracks/domains`      :doc:`tracks/bed`          :doc:`tracks/gtf`          :doc:`tracks/narrow_peak`  :doc:`tracks/bigwig`       :doc:`tracks/bedgraph`     :doc:`tracks/bedgraph_mat  :doc:`tracks/hlines`       :doc:`tracks/hic_matrix`   :doc:`tracks/scalebar`   
 =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================  =========================
 overlay_previous           no                         no                         no                         no                         no                         no                         no                         no                         no                         no                         no                         no                         no                       
 where                      bottom                                                                                                                                                                                                                                                                                                                              left                     

docs/content/all_possible_properties.txt

@@ -1,10 +1,10 @@
 - **overlay_previous**:
 
-  - for *x-axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, scalebar, spacer*: no, yes, share-y
+  - for *x_axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, scalebar, spacer*: no, yes, share-y
 
 - **where**:
 
-  - for *x-axis*: top, bottom
+  - for *x_axis*: top, bottom
 
   - for *scalebar*: left, right, top, bottom
 

docs/content/all_tracks.rst

@@ -28,4 +28,4 @@ All available tracks
 
 :doc:`tracks/spacer`
 
-:doc:`tracks/x-axis`
+:doc:`tracks/x_axis`

docs/content/tracks/x_axis.rst

@@ -0,0 +1,20 @@
+x_axis
+==========
+
+Description
+-----------
+
+A track to include a x axis. To use it you can either put ``file_type = x_axis`` or call your section ``[x-axis]``
+
+Parameters
+----------
+
+.. include:: auto/x_axis_deduced_from_code.txt
+
+Output of ``make_tracks_file``:
+-------------------------------
+
+.. literalinclude:: auto/x_axis_options_text.txt
+    :language: INI
+
+

pygenometracks/getAllDefaultsAndPossible.py

@@ -46,7 +46,7 @@
 
 def main():
     all_tracks = PlotTracks.get_available_tracks()
-    my_prefered_order_tracks_names = ['x-axis', 'epilogos', 'links',
+    my_prefered_order_tracks_names = ['x_axis', 'epilogos', 'links',
                                       'domains', 'bed', 'gtf', 'narrow_peak',
                                       'bigwig', 'bedgraph', 'bedgraph_matrix',
                                       'hlines', 'hic_matrix', 'scalebar']
@@ -161,7 +161,7 @@ def main():
                 fo.write("- **height**: If you do not set it, the height will "
                          "be adjusted so that each bin is a square, else you "
                          "can choose any float above 0.\n\n")
-            elif track_type == "x-axis":
+            elif track_type == "x_axis":
                 fo.write("- **height**: If you do not set it, the height will "
                          "be ``fontsize / 8``, else you "
                          "can choose any float above 0.\n\n")

pygenometracks/tracksClass.py

@@ -145,7 +145,7 @@ def get_tracks_height(self, start_region=None, end_region=None):
                 continue
             elif 'height' in track_dict:
                 height = track_dict['height']
-            elif track_dict['file_type'] == 'x-axis':
+            elif track_dict['file_type'] == 'x_axis':
                 height = track_dict['fontsize'] / 8
             elif 'depth' in track_dict and \
                  track_dict['file_type'] == 'hic_matrix':
@@ -374,7 +374,7 @@ def parse_tracks(self, tracks_file):
                 track_options['file_type'] = 'spacer'
                 track_options['track_class'] = SpacerTrack
             elif section_name.endswith('[x-axis]'):
-                track_options['file_type'] = 'x-axis'
+                track_options['file_type'] = 'x_axis'
                 track_options['track_class'] = XAxisTrack
             # For the others we need to have a 'file_type'
             # Either the file_type is part of the keywords
@@ -642,7 +642,7 @@ def plot_y_axis(self, ax, plot_ax):
 
 class XAxisTrack(GenomeTrack):
     SUPPORTED_ENDINGS = []
-    TRACK_TYPE = 'x-axis'
+    TRACK_TYPE = 'x_axis'
     NECESSARY_PROPERTIES = []
     DEFAULTS_PROPERTIES = {'where': 'bottom',
                            'fontsize': 15}