hybkit.plot

Methods for plotting analyses of HybRecord and FoldRecord Objects.

hybkit.plot.hybrid_type_count(plot_file_name, analysis_dict, name=None, title='Hybrid Types', other_threshhold=0.1, min_wedge_size=0.04, plot_file_type='png', dpi=600, matplotlib_settings={'autopct': '%1.1f%%', 'counterclock': False, 'shadow': False, 'startangle': 90})

Plot the counts of types resulting from the Type Analysis.

Parameters:
  • plot_file_name (str) – File name for output plots.
  • analysis_dict (dict) – Dict from type analysis (see type_dict()).
  • title (str, optional) – Title / header for plot.
  • other_threshhold (float, optional) – Total fraction at which to begin the “other” wedge. Setting to 0.0 disables the “other” wedge based on a threshhold.
  • min_wedge_size (float, optional) – Minimum wedge fraction at which to add to the “other” wedge. Setting to 0.0 disables the “other” wedge based on minimum wedge size.
  • plot_file_type (str, optional) – File type for saving of plots. Options: {‘png’, ‘ps’, ‘pdf’, ‘svg’}
  • dpi (int, optional) – DPI for saving of plots.
  • matplotlib_settings (dict, optional) – Dict of keys and values of settings to pass to the matplotlib.plot() function
hybkit.plot.all_seg_type(plot_file_name, analysis_dict, name=None, title='Total Segment Portions', other_threshhold=0.1, min_wedge_size=0.04, plot_file_type='png', dpi=600, matplotlib_settings={'autopct': '%1.1f%%', 'counterclock': False, 'shadow': False, 'startangle': 90})

Plot the counts of segment types resulting from the Type Analysis.

Parameters:
  • plot_file_name (str) – File name for output plot.
  • analysis_dict (dict) – Dict from type analysis (see type_dict()).
  • title (str, optional) – Title / header for plot.
  • other_threshhold (float, optional) – Total fraction at which to begin the “other” wedge. Setting to 0.0 disables the “other” wedge based on a threshhold.
  • min_wedge_size (float, optional) – Minimum wedge fraction at which to add to the “other” wedge. Setting to 0.0 disables the “other” wedge based on minimum wedge size.
  • plot_file_type (str, optional) – File type for saving of plots. Options: {‘png’, ‘ps’, ‘pdf’, ‘svg’}
  • dpi (int, optional) – DPI for saving of plots.
  • matplotlib_settings (dict, optional) – Dict of keys and values of settings to pass to the matplotlib.plot() function.
hybkit.plot.mirna_count(plot_file_name, analysis_dict, name=None, title='Hybrid Types', other_threshhold=0.1, min_wedge_size=0.04, plot_file_type='png', dpi=600, matplotlib_settings={'autopct': '%1.1f%%', 'counterclock': False, 'shadow': False, 'startangle': 90})

Plot the results of the miRNA Count Analysis.

Parameters:
  • plot_file_name (str) – File name for output plot.
  • analysis_dict (dict) – Dict from mirna count analysis (see mirna_count_dict()).
  • title (str, optional) – Title / header for plot.
  • other_threshhold (float, optional) – Total fraction at which to begin the “other” wedge. Setting to 0.0 disables the “other” wedge based on a threshhold.
  • min_wedge_size (float, optional) – Minimum wedge fraction at which to add to the “other” wedge. Setting to 0.0 disables the “other” wedge based on minimum wedge size.
  • plot_file_type (str, optional) – File type for saving of plots. Options: {‘png’, ‘ps’, ‘pdf’, ‘svg’}
  • dpi (int, optional) – DPI for saving of plots.
  • matplotlib_settings (dict, optional) – Dict of keys and values of settings to pass to the matplotlib.plot() function.
hybkit.plot.mirna_target(plot_file_name, mirna_name, mirna_targets_dict, title=None, name=None, other_threshhold=0.1, min_wedge_size=0.04, plot_file_type='png', dpi=600, matplotlib_settings={'autopct': '%1.1f%%', 'counterclock': False, 'shadow': False, 'startangle': 90})

Plot the targets of a single mirna from the miRNA Target Analysis.

Parameters:
  • plot_file_name (str) – File name for output plot.
  • mirna_name (str) – Name of miRNA to plot for title.
  • mirna_targets_dict (dict) – Dict from mirna_target analysis (see mirna_target_dict()).
  • title (str, optional) – Title / header for plot (replaces default title).
  • name (str, optional) – Data source name to prepend to title.
  • other_threshhold (float, optional) – Total fraction at which to begin the “other” wedge. Setting to 0.0 disables the “other” wedge based on a threshhold.
  • min_wedge_size (float, optional) – Minimum wedge fraction at which to add to the “other” wedge. Setting to 0.0 disables the “other” wedge based on minimum wedge size.
  • plot_file_type (str, optional) – File type for saving of plots. Options: {‘png’, ‘ps’, ‘pdf’, ‘svg’}
  • dpi (int, optional) – DPI for saving of plots.
  • matplotlib_settings (dict, optional) – Dict of keys and values of settings to pass to the matplotlib.plot() function.
hybkit.plot.mirna_target_type(plot_file_name, mirna_name, mirna_target_type_counts_dict, title=None, name=None, other_threshhold=0.1, min_wedge_size=0.04, plot_file_type='png', dpi=600, matplotlib_settings={'autopct': '%1.1f%%', 'counterclock': False, 'shadow': False, 'startangle': 90})

Plot the targets types of a single mirna from the miRNA Target Analysis.

Parameters:
  • plot_file_name (str) – File name for output plot.
  • mirna_name (str) – Name of miRNA to plot for title.
  • mirna_targets_dict (dict) – Dict from mirna_target analysis (see mirna_target_dict()).
  • title (str, optional) – Title / header for plot (replaces default title).
  • name (str, optional) – Data source name to prepend to title.
  • other_threshhold (float, optional) – Total fraction at which to begin the “other” wedge. Setting to 0.0 disables the “other” wedge based on a threshhold.
  • min_wedge_size (float, optional) – Minimum wedge fraction at which to add to the “other” wedge. Setting to 0.0 disables the “other” wedge based on minimum wedge size.
  • plot_file_type (str, optional) – File type for saving of plots. Options: {‘png’, ‘ps’, ‘pdf’, ‘svg’}
  • dpi (int, optional) – DPI for saving of plots.
  • matplotlib_settings (dict, optional) – Dict of keys and values of settings to pass to the matplotlib.plot() function.
hybkit.plot.mirna_fold(plot_file_name, fold_analysis_dict, title=None, name=None, data_format='-', min_fraction_size=0.01, plot_file_type='png', dpi=600, matplotlib_settings={'axes.labelsize': 'large', 'axes.titlesize': 'x-large', 'xtick.labelsize': 'large', 'ytick.labelsize': 'large'})

Plot the bound percentage of mirna by base from the miRNA Fold Analysis.

Parameters:
  • plot_file_name (str) – File name for output plot.
  • fold_analysis_dict (dict) – Dict from mirna_fold analysis (see mirna_fold_dict()).
  • title (str, optional) – Title / header for plot (replaces default title).
  • name (str, optional) – Data source name to prepend to title.
  • data_format (str, optional) – matplotlib line/data format.
  • min_fractione_size (float, optional) – Minimum fraction to include at tail end of plot. Setting to 0 includes all bases evaluated.
  • plot_file_type (str, optional) – File type for saving of plots. Options: {‘png’, ‘ps’, ‘pdf’, ‘svg’}
  • dpi (int, optional) – DPI for saving of plots.
  • matplotlib_settings (dict, optional) – Dict of keys and values of settings to pass to the matplotlib.plot() function.