From 0f47ccc6ef1f7c4930a18788edfcfaf571993a4f Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 14 Jul 2016 18:55:23 -0400 Subject: [PATCH] add DPI option as parameter for plot_coverage --- reports.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/reports.py b/reports.py index 99bf159da..99ff054b1 100755 --- a/reports.py +++ b/reports.py @@ -429,6 +429,13 @@ def parser_plot_coverage_common(parser=argparse.ArgumentParser()): # parser n type=int, help="Width of the plot in pixels (default: %(default)s)" ) + parser.add_argument( + '--plotDPI', + dest="plot_dpi", + default=plt.gcf().get_dpi(), + type=int, + help="dots per inch for rendered output, more useful for vector modes (default: %(default)s)" + ) parser.add_argument( '--plotTitle', dest="plot_title", @@ -472,6 +479,7 @@ def plot_coverage( plot_style, plot_width, plot_height, + plot_dpi, plot_title, base_q_threshold, mapping_q_threshold, @@ -534,12 +542,11 @@ def plot_coverage( domain_max = 0 with plt.style.context(plot_style): - fig = plt.gcf() - DPI = fig.get_dpi() + DPI = plot_dpi or fig.get_dpi() fig.set_size_inches(float(plot_width) / float(DPI), float(plot_height) / float(DPI)) - font_size = math.sqrt((plot_width**2) + (plot_height**2)) / float(DPI) * 1.25 + font_size = (2.5 * plot_height) / float(DPI) ax = plt.subplot() # Defines ax variable by creating an empty plot @@ -607,6 +614,7 @@ def align_and_plot_coverage( plot_style, plot_width, plot_height, + plot_dpi, plot_title, base_q_threshold, mapping_q_threshold, @@ -662,7 +670,7 @@ def align_and_plot_coverage( # -- call plot function -- plot_coverage( - bam_aligned, out_plot_file, plot_format, plot_data_style, plot_style, plot_width, plot_height, plot_title, + bam_aligned, out_plot_file, plot_format, plot_data_style, plot_style, plot_width, plot_height, plot_dpi, plot_title, base_q_threshold, mapping_q_threshold, max_coverage_depth, read_length_threshold, out_summary )