diff --git a/README.md b/README.md index a5ccb248..a0320634 100644 --- a/README.md +++ b/README.md @@ -753,7 +753,7 @@ Plotting: --type {features,cog} Plot type: feature/cog (default = features) --label LABEL Plot center label (for line breaks use '|') - --size {4,8,16} Plot size in inches: 4/8/16 (default = 4) + --size {4,8,16} Plot size in inches: 4/8/16 (default = 8) --dpi {150,300,600} Plot resolution as dots per inch: 150/300/600 (default = 300) General: diff --git a/bakta/plot.py b/bakta/plot.py index 0ab5ad84..133e3084 100644 --- a/bakta/plot.py +++ b/bakta/plot.py @@ -90,7 +90,7 @@ def main(): arg_group_plot.add_argument('--sequences', action='store', default='all', help='Sequences to plot: comma separated number or name (default = all, numbers one-based)') arg_group_plot.add_argument('--type', action='store', type=str, default=bc.PLOT_FEATURES, choices=[bc.PLOT_FEATURES, bc.PLOT_COG], help=f'Plot type (default = {bc.PLOT_FEATURES})') arg_group_plot.add_argument('--label', action='store', type=str, default=None, help=f"Plot center label (for line breaks use '|')") - arg_group_plot.add_argument('--size', action='store', type=int, default=4, choices=[4, 8, 16], help='Plot size in inches: 4/8/16 (default = 4)') + arg_group_plot.add_argument('--size', action='store', type=int, default=8, choices=[4, 8, 16], help='Plot size in inches: 4/8/16 (default = 8)') arg_group_plot.add_argument('--dpi', action='store', type=int, default=300, choices=[150, 300, 600], help='Plot resolution as dots per inch: 150/300/600 (default = 300)') arg_group_general = parser.add_argument_group('General') @@ -232,7 +232,7 @@ def main(): write(data, features, output_path, colors, plot_name_suffix=plot_name_suffix, plot_type=plot_type, plot_label=plot_label, plot_size=plot_size, plot_dpi=plot_dpi) -def write(data, features, output_path, colors=COLORS, plot_name_suffix=None, plot_type=bc.PLOT_FEATURES, plot_label=None, plot_size=4, plot_dpi=300): +def write(data, features, output_path, colors=COLORS, plot_name_suffix=None, plot_type=bc.PLOT_FEATURES, plot_label=None, plot_size=8, plot_dpi=300): sequence_list = insdc.build_biopython_sequence_list(data, features) for seq in sequence_list: # fix edge features because PyCirclize cannot handle them correctly seq.features = [feat for feat in seq.features if feat.type != 'gene' and feat.type != 'source']