Merge pull request #198 from lldelisle/updateArgParse

Update arg parse

README.md

@@ -90,7 +90,7 @@ optional arguments:
                         plot, in BED format, can be given. If this is the
                         case, multiple files will be created using a prefix
                         the value of --outFileName
-  --width WIDTH         figure width in centimeters
+  --width WIDTH         figure width in centimeters (default is 40)
   --height HEIGHT       Figure height in centimeters. If not given, the figure
                         height is computed based on the heights of the tracks.
                         If given, the track height are proportionally scaled
@@ -100,9 +100,10 @@ optional arguments:
   --outFileName OUTFILENAME, -out OUTFILENAME
                         File name to save the image, file prefix in case
                         multiple images are stored
-  --fontSize FONTSIZE   Font size for the labels of the plot
+  --fontSize FONTSIZE   Font size for the labels of the plot (default is 0.3 *
+                        figure width)
   --dpi DPI             Resolution for the image in case the ouput is a raster
-                        graphics image (e.g png, jpg)
+                        graphics image (e.g png, jpg) (default is 72)
   --trackLabelFraction TRACKLABELFRACTION
                         By default the space dedicated to the track labels is
                         0.05 of the plot width. This fraction can be changed

pygenometracks/plotTracks.py

@@ -150,15 +150,7 @@
 from pygenometracks._version import __version__
 from .utilities import InputError
 
-DEFAULT_BED_COLOR = '#1f78b4'
-DEFAULT_BIGWIG_COLOR = '#33a02c'
-DEFAULT_BEDGRAPH_COLOR = '#a6cee3'
-DEFAULT_MATRIX_COLORMAP = 'RdYlBu_r'
-DEFAULT_TRACK_HEIGHT = 3  # in centimeters
 DEFAULT_FIGURE_WIDTH = 40  # in centimeters
-# proportion of width dedicated to (figure, legends)
-# DEFAULT_WIDTH_RATIOS = (0.95, 0.05)
-DEFAULT_MARGINS = {'left': 0.04, 'right': 0.92, 'bottom': 0.12, 'top': 0.9}
 
 
 def parse_arguments(args=None):
@@ -189,7 +181,7 @@ def parse_arguments(args=None):
                        )
 
     parser.add_argument('--width',
-                        help='figure width in centimeters',
+                        help='figure width in centimeters (default is {})'.format(DEFAULT_FIGURE_WIDTH),
                         type=float,
                         default=DEFAULT_FIGURE_WIDTH)
 
@@ -209,13 +201,12 @@ def parse_arguments(args=None):
                         required=True)
 
     parser.add_argument('--fontSize',
-                        help='Font size for the labels of the plot',
-                        type=float,
-                        )
+                        help='Font size for the labels of the plot (default is 0.3 * figure width)',
+                        type=float)
 
     parser.add_argument('--dpi',
                         help='Resolution for the image in case the'
-                             ' ouput is a raster graphics image (e.g png, jpg)',
+                             ' ouput is a raster graphics image (e.g png, jpg) (default is 72)',
                         type=int,
                         default=72
                         )