diff --git a/riboplot/riboplot.py b/riboplot/riboplot.py index 7a6a702..196e96c 100644 --- a/riboplot/riboplot.py +++ b/riboplot/riboplot.py @@ -120,9 +120,9 @@ def get_color_palette(scheme): """ color_schemes = { 'default': { - 'frames': ['tomato', 'limegreen', 'deepskyblue'], 'background': '#fafafa', - 'color': '#616161', 'ticks': '#757575', 'start': '#ffffff', 'stop': '#919191', - 'rna': '#e0e0e0', 'axis': '#e0e0e0', 'grey': '#bdbdbd' + 'frames': ['tomato', 'limegreen', 'deepskyblue'], 'background': '#ffffff', + 'color': '#616161', 'ticks': '#757575', 'start': '#ffffff', 'stop': '#909090', + 'rna': '#eaeaea', 'axis': '#e0e0e0', 'grey': '#bdbdbd' }, 'colorbrewer': { 'frames': ['#fc8d62', '#66c2a5', '#8da0cb'] @@ -169,7 +169,7 @@ def plot_profile(ribo_counts, transcript_name, transcript_length, ax_rna = ax2.twinx() ax_rna.set_ylabel('RNA-Seq count', fontdict=font_axis, labelpad=10) ax_rna.bar(rna_counts.keys(), rna_counts.values(), facecolor=colors['rna'], - edgecolor=colors['rna'], label='RNA', linewidth=0) + edgecolor=colors['rna'], label='RNA') ax_rna.set_zorder(1) frame_counts = {1: {}, 2: {}, 3: {}} @@ -192,7 +192,7 @@ def plot_profile(ribo_counts, transcript_name, transcript_length, x_vals = [pos + read_offset for pos in frame_counts[frame].keys()] else: x_vals = frame_counts[frame].keys() - ax2.bar(x_vals, frame_counts[frame].values(), color=color, facecolor=color, edgecolor=color, linewidth=0) + ax2.bar(x_vals, frame_counts[frame].values(), color=color, facecolor=color, edgecolor=color) # ORF architecture gs3 = gridspec.GridSpecFromSubplotSpec(3, 1, subplot_spec=gs[1], hspace=0.1) @@ -258,11 +258,11 @@ def plot_profile(ribo_counts, transcript_name, transcript_length, starts = [(item, 1) for item in start_stops[frame]['starts']] stops = [(item, 1) for item in start_stops[frame]['stops']] start_colors = [colors['start'] for item in starts] - axis.broken_barh(starts, (0.11, 0.2), - facecolors=start_colors, edgecolors=start_colors, label='start', zorder=5, linewidth=0) + axis.broken_barh(starts, (0.11, 0.2), facecolors=start_colors, + edgecolors=start_colors, label='start', zorder=5) stop_colors = [colors['stop'] for item in stops] axis.broken_barh(stops, (0, 0.2), facecolors=stop_colors, - edgecolors=stop_colors, label='stop', zorder=5, linewidth=0) + edgecolors=stop_colors, label='stop', zorder=5) axis.set_ylabel('{}'.format(frame), fontdict={'family': 'sans-serif', 'color': colors['color'], 'weight': 'normal', 'size': '6'},