Index

A

abs_x_thresh (bioviz.configs.VolcanoConfig attribute) add_pvalue_annotation() (in module bioviz.plots.km) additional_values_to_label (bioviz.configs.VolcanoConfig attribute) adjust (bioviz.configs.VolcanoConfig attribute) alpha_threshold (bioviz.configs.ForestPlotConfig attribute) annotate() (bioviz.plots.VolcanoPlotter method) annotation_fontweight_nonsig (bioviz.configs.VolcanoConfig attribute) annotation_fontweight_sig (bioviz.configs.VolcanoConfig attribute) annotation_nonsig_color (bioviz.configs.VolcanoConfig attribute)

annotation_sig_color (bioviz.configs.VolcanoConfig attribute) annotation_sig_down_color (bioviz.configs.VolcanoConfig attribute) annotation_sig_up_color (bioviz.configs.VolcanoConfig attribute) apply_post_row_group_shift (bioviz.configs.OncoplotConfig attribute) aspect (bioviz.configs.OncoplotConfig attribute) attach_to_marker_edge (bioviz.configs.VolcanoConfig attribute) auto_adjust_cell_size (bioviz.configs.OncoplotConfig attribute) auto_expand_for_legend (bioviz.configs.KMPlotConfig attribute) ax (bioviz.configs.VolcanoConfig attribute) axis_label_fontsize (bioviz.configs.VolcanoConfig attribute)

B

bar_buffer (bioviz.configs.OncoplotConfig attribute) bar_offset (bioviz.configs.OncoplotConfig attribute) bar_offset_use_points (bioviz.configs.OncoplotConfig attribute) bar_width (bioviz.configs.OncoplotConfig attribute)

bar_width_points (bioviz.configs.OncoplotConfig attribute) bar_width_use_points (bioviz.configs.OncoplotConfig attribute) bioviz.plots.km module

C

capsize (bioviz.configs.ForestPlotConfig attribute) category_order (bioviz.configs.ForestPlotConfig attribute) cell_aspect (bioviz.configs.OncoplotConfig attribute) censor_marker (bioviz.configs.KMPlotConfig attribute) censor_markeredgewidth (bioviz.configs.KMPlotConfig attribute) censor_markersize (bioviz.configs.KMPlotConfig attribute) center_around_null (bioviz.configs.ForestPlotConfig attribute) ci_alpha (bioviz.configs.KMPlotConfig attribute) ci_lower_col (bioviz.configs.ForestPlotConfig attribute) ci_style (bioviz.configs.KMPlotConfig attribute) ci_upper_col (bioviz.configs.ForestPlotConfig attribute) close() (bioviz.plots.TablePlotter method) (bioviz.plots.VolcanoPlotter method) col_sort_by (bioviz.configs.OncoplotConfig attribute) col_split_by (bioviz.configs.OncoplotConfig attribute) col_split_gap (bioviz.configs.OncoplotConfig attribute) col_split_order (bioviz.configs.OncoplotConfig attribute) color_dict (bioviz.configs.KMPlotConfig attribute) color_mode (bioviz.configs.VolcanoConfig attribute)

color_nonsignificant (bioviz.configs.ForestPlotConfig attribute) color_risktable_counts (bioviz.configs.KMPlotConfig attribute) color_significant (bioviz.configs.ForestPlotConfig attribute) column_label_fontsize (bioviz.configs.OncoplotConfig attribute) compute_y_positions() (bioviz.plots.ForestPlotter method) conf_type (bioviz.configs.KMPlotConfig attribute) config (bioviz.plots.ForestPlotter attribute) (bioviz.plots.KMPlotter attribute) connector_color (bioviz.configs.VolcanoConfig attribute) connector_color_left (bioviz.configs.VolcanoConfig attribute) connector_color_nonsig (bioviz.configs.VolcanoConfig attribute) connector_color_nonsig_left (bioviz.configs.VolcanoConfig attribute) connector_color_nonsig_right (bioviz.configs.VolcanoConfig attribute) connector_color_right (bioviz.configs.VolcanoConfig attribute) connector_color_sig (bioviz.configs.VolcanoConfig attribute) connector_color_sig_left (bioviz.configs.VolcanoConfig attribute) connector_color_sig_right (bioviz.configs.VolcanoConfig attribute) connector_color_use_point_color (bioviz.configs.VolcanoConfig attribute) connector_width (bioviz.configs.VolcanoConfig attribute)

D

data (bioviz.plots.ForestPlotter attribute) (bioviz.plots.KMPlotter attribute)

direction_col (bioviz.configs.VolcanoConfig attribute) direction_colors (bioviz.configs.VolcanoConfig attribute)

E

event_col (bioviz.configs.KMPlotConfig attribute) explicit_label_adjustable (bioviz.configs.VolcanoConfig attribute)

explicit_label_positions (bioviz.configs.VolcanoConfig attribute) explicit_label_replace (bioviz.configs.VolcanoConfig attribute)

F

fig_bottom_margin (bioviz.configs.OncoplotConfig attribute) fig_height (bioviz.configs.KMPlotConfig attribute) fig_title (bioviz.configs.OncoplotConfig attribute) fig_title_fontsize (bioviz.configs.OncoplotConfig attribute) fig_top_margin (bioviz.configs.OncoplotConfig attribute) fig_width (bioviz.configs.KMPlotConfig attribute) fig_y_margin (bioviz.configs.OncoplotConfig attribute) figsize (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.OncoplotConfig attribute) (bioviz.configs.VolcanoConfig attribute)

figure_facecolor (bioviz.configs.OncoplotConfig attribute) figure_transparent (bioviz.configs.OncoplotConfig attribute) fontsize_nonsig (bioviz.configs.VolcanoConfig attribute) fontsize_sig (bioviz.configs.VolcanoConfig attribute) force_label_side_by_point_sign (bioviz.configs.VolcanoConfig attribute) force_labels_adjustable (bioviz.configs.VolcanoConfig attribute) force_show_censors (bioviz.configs.KMPlotConfig attribute) ForestPlotConfig (class in bioviz.configs) ForestPlotter (class in bioviz.plots) format_pvalue() (in module bioviz.plots.km) from_dict() (bioviz.plots.VolcanoPlotter class method)

G

get_dynamic_bar_x() (bioviz.plots.OncoPlotter method) get_figsize() (bioviz.configs.KMPlotConfig method) get_xlabel() (bioviz.configs.KMPlotConfig method) get_ylabel() (bioviz.configs.KMPlotConfig method)

group_col (bioviz.configs.KMPlotConfig attribute) group_label_kwargs (bioviz.configs.VolcanoConfig attribute) group_label_top (bioviz.configs.VolcanoConfig attribute) group_order (bioviz.configs.KMPlotConfig attribute)

H

heatmap_annotation (bioviz.configs.OncoplotConfig attribute) heatmap_bottom_left_triangle_values (bioviz.configs.OncoplotConfig attribute)

heatmap_upper_right_triangle_values (bioviz.configs.OncoplotConfig attribute) horiz_offset_range (bioviz.configs.VolcanoConfig attribute) hr_col (bioviz.configs.ForestPlotConfig attribute)

K

KMPlotConfig (class in bioviz.configs)

KMPlotter (class in bioviz.plots)

L

label_col (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute) label_fontsize (bioviz.configs.KMPlotConfig attribute) label_mode (bioviz.configs.VolcanoConfig attribute) label_more() (bioviz.plots.VolcanoPlotter method) label_offset (bioviz.configs.VolcanoConfig attribute) label_offset_mode (bioviz.configs.VolcanoConfig attribute) legend_bbox_to_anchor (bioviz.configs.OncoplotConfig attribute) legend_category_order (bioviz.configs.OncoplotConfig attribute) legend_fontsize (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.OncoplotConfig attribute) legend_frameon (bioviz.configs.KMPlotConfig attribute) legend_label_max_lines (bioviz.configs.KMPlotConfig attribute) legend_label_overrides (bioviz.configs.KMPlotConfig attribute) legend_label_wrap_chars (bioviz.configs.KMPlotConfig attribute)

legend_linewidth_scale (bioviz.configs.KMPlotConfig attribute) legend_loc (bioviz.configs.KMPlotConfig attribute) legend_markerscale (bioviz.configs.KMPlotConfig attribute) legend_offset (bioviz.configs.OncoplotConfig attribute) legend_offset_points (bioviz.configs.OncoplotConfig attribute) legend_offset_use_points (bioviz.configs.OncoplotConfig attribute) legend_show_n (bioviz.configs.KMPlotConfig attribute) legend_title (bioviz.configs.KMPlotConfig attribute) legend_title_fontsize (bioviz.configs.OncoplotConfig attribute) legend_title_fontweight (bioviz.configs.KMPlotConfig attribute) linestyle (bioviz.configs.KMPlotConfig attribute) linewidth (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) log_scale (bioviz.configs.ForestPlotConfig attribute) log_transform_ycol (bioviz.configs.VolcanoConfig attribute)

M

marker_color_nonsignificant (bioviz.configs.ForestPlotConfig attribute) marker_color_significant (bioviz.configs.ForestPlotConfig attribute) marker_size (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute) marker_style (bioviz.configs.ForestPlotConfig attribute) model_config (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.OncoplotConfig attribute) (bioviz.configs.VolcanoConfig attribute)

model_post_init() (bioviz.configs.OncoplotConfig method) module bioviz.plots.km move_row_group_labels() (bioviz.plots.OncoPlotter method)

N

nudge_padding_pixels (bioviz.configs.VolcanoConfig attribute)

O

OncoplotConfig (class in bioviz.configs)

OncoPlotter (class in bioviz.plots)

P

pad_by_marker (bioviz.configs.VolcanoConfig attribute) palette (bioviz.configs.VolcanoConfig attribute) per_patient_censor_markers (bioviz.configs.KMPlotConfig attribute) plot() (bioviz.plots.ForestPlotter method) (bioviz.plots.KMPlotter method) (bioviz.plots.OncoPlotter method) (bioviz.plots.TablePlotter method) (bioviz.plots.VolcanoPlotter method)

prepare_data() (bioviz.plots.ForestPlotter method) pval_loc (bioviz.configs.KMPlotConfig attribute) pvalue_box (bioviz.configs.KMPlotConfig attribute) pvalue_col (bioviz.configs.ForestPlotConfig attribute) pvalue_fontsize (bioviz.configs.KMPlotConfig attribute)

R

redraw_row_group_labels() (bioviz.plots.OncoPlotter static method) reference_col (bioviz.configs.ForestPlotConfig attribute) reference_line_color (bioviz.configs.ForestPlotConfig attribute) reference_line_style (bioviz.configs.ForestPlotConfig attribute) reference_line_width (bioviz.configs.ForestPlotConfig attribute) remove_unused_keys_in_legend (bioviz.configs.OncoplotConfig attribute) resolve_labels() (bioviz.plots.VolcanoPlotter method) risktable_fontsize (bioviz.configs.KMPlotConfig attribute) risktable_hspace (bioviz.configs.KMPlotConfig attribute) risktable_label_max_lines (bioviz.configs.KMPlotConfig attribute) risktable_label_overrides (bioviz.configs.KMPlotConfig attribute) risktable_label_wrap_chars (bioviz.configs.KMPlotConfig attribute) risktable_min_rows (bioviz.configs.KMPlotConfig attribute) risktable_row_spacing (bioviz.configs.KMPlotConfig attribute) risktable_title_fontsize (bioviz.configs.KMPlotConfig attribute)

risktable_title_gap_factor (bioviz.configs.KMPlotConfig attribute) rotate_left_annotation_label (bioviz.configs.OncoplotConfig attribute) row_group_col (bioviz.configs.OncoplotConfig attribute) row_group_label_fontsize (bioviz.configs.OncoplotConfig attribute) row_group_label_gap (bioviz.configs.OncoplotConfig attribute) row_group_label_gap_use_points (bioviz.configs.OncoplotConfig attribute) row_group_order (bioviz.configs.OncoplotConfig attribute) row_group_post_bar_shift (bioviz.configs.OncoplotConfig attribute) row_group_post_bar_shift_points (bioviz.configs.OncoplotConfig attribute) row_group_post_label_shift (bioviz.configs.OncoplotConfig attribute) row_group_post_label_shift_points (bioviz.configs.OncoplotConfig attribute) row_group_post_shift_use_points (bioviz.configs.OncoplotConfig attribute) row_label_fontsize (bioviz.configs.OncoplotConfig attribute) row_split_gap (bioviz.configs.OncoplotConfig attribute) row_values_color_dict (bioviz.configs.OncoplotConfig attribute) rowlabel_use_points (bioviz.configs.OncoplotConfig attribute)

S

save() (bioviz.plots.TablePlotter method) (bioviz.plots.VolcanoPlotter method) save_bbox_inches (bioviz.configs.KMPlotConfig attribute) section_gap (bioviz.configs.ForestPlotConfig attribute) section_label_x_position (bioviz.configs.ForestPlotConfig attribute) section_labels (bioviz.configs.ForestPlotConfig attribute) section_separator_alpha (bioviz.configs.ForestPlotConfig attribute) section_separator_color (bioviz.configs.ForestPlotConfig attribute) set_data() (bioviz.plots.TablePlotter method) (bioviz.plots.VolcanoPlotter method) shift_row_group_bars_and_labels() (bioviz.plots.OncoPlotter method) show_caps (bioviz.configs.ForestPlotConfig attribute)

show_ci (bioviz.configs.KMPlotConfig attribute) show_grid (bioviz.configs.ForestPlotConfig attribute) show_pvalue (bioviz.configs.KMPlotConfig attribute) show_reference_line (bioviz.configs.ForestPlotConfig attribute) show_risktable (bioviz.configs.KMPlotConfig attribute) show_section_separators (bioviz.configs.ForestPlotConfig attribute) show_stats_table (bioviz.configs.ForestPlotConfig attribute) show_y_spine (bioviz.configs.ForestPlotConfig attribute) show_yticks (bioviz.configs.ForestPlotConfig attribute) spacing_aspect_scale (bioviz.configs.OncoplotConfig attribute) stats_fontsize (bioviz.configs.ForestPlotConfig attribute) stats_table_col_spacing (bioviz.configs.ForestPlotConfig attribute) stats_table_x_position (bioviz.configs.ForestPlotConfig attribute)

T

TablePlotter (class in bioviz.plots) target_cell_height (bioviz.configs.OncoplotConfig attribute) target_cell_width (bioviz.configs.OncoplotConfig attribute) thresh_line_color (bioviz.configs.VolcanoConfig attribute) thresh_line_style (bioviz.configs.VolcanoConfig attribute) thresh_line_width (bioviz.configs.VolcanoConfig attribute) tick_label_fontsize (bioviz.configs.VolcanoConfig attribute) time_col (bioviz.configs.KMPlotConfig attribute) timeline (bioviz.configs.KMPlotConfig attribute) title (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute)

title_fontsize (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute) title_fontweight (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute) to_dict() (bioviz.plots.VolcanoPlotter method) top_annotation_inter_spacer (bioviz.configs.OncoplotConfig attribute) top_annotation_intra_spacer (bioviz.configs.OncoplotConfig attribute) top_annotation_label_offset (bioviz.configs.OncoplotConfig attribute) top_annotation_label_offset_points (bioviz.configs.OncoplotConfig attribute) top_annotation_label_use_points (bioviz.configs.OncoplotConfig attribute) top_annotation_order (bioviz.configs.OncoplotConfig attribute) top_annotations (bioviz.configs.OncoplotConfig attribute)

U

update_config() (bioviz.plots.TablePlotter method) (bioviz.plots.VolcanoPlotter method)

use_adjust_text (bioviz.configs.VolcanoConfig attribute)

V

value_col (bioviz.configs.OncoplotConfig attribute) value_legend_title (bioviz.configs.OncoplotConfig attribute) values_to_label (bioviz.configs.VolcanoConfig attribute)

variable_col (bioviz.configs.ForestPlotConfig attribute) vert_jitter_range (bioviz.configs.VolcanoConfig attribute) VolcanoConfig (class in bioviz.configs) VolcanoPlotter (class in bioviz.plots)

X

x_col (bioviz.configs.OncoplotConfig attribute) (bioviz.configs.VolcanoConfig attribute) x_label (bioviz.configs.VolcanoConfig attribute) x_thresh (bioviz.configs.VolcanoConfig attribute) x_thresh_line_color (bioviz.configs.VolcanoConfig attribute) x_thresh_line_style (bioviz.configs.VolcanoConfig attribute) x_thresh_line_width (bioviz.configs.VolcanoConfig attribute) xlab (bioviz.configs.KMPlotConfig attribute) xlabel (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) xlabel_fontsize (bioviz.configs.ForestPlotConfig attribute) xlim (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute)

xtick_aspect_scale (bioviz.configs.OncoplotConfig attribute) xtick_fontsize (bioviz.configs.ForestPlotConfig attribute) xtick_interval_months (bioviz.configs.KMPlotConfig attribute) xtick_step (bioviz.configs.VolcanoConfig attribute) xticklabel_use_points (bioviz.configs.OncoplotConfig attribute) xticklabel_xoffset (bioviz.configs.OncoplotConfig attribute) xticklabel_yoffset (bioviz.configs.OncoplotConfig attribute) xticks (bioviz.configs.ForestPlotConfig attribute) (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute)

Y

y_col (bioviz.configs.OncoplotConfig attribute) (bioviz.configs.VolcanoConfig attribute) y_col_thresh (bioviz.configs.VolcanoConfig attribute) y_label (bioviz.configs.VolcanoConfig attribute) y_margin (bioviz.configs.ForestPlotConfig attribute) y_thresh (bioviz.configs.VolcanoConfig attribute) y_thresh_line_color (bioviz.configs.VolcanoConfig attribute) y_thresh_line_style (bioviz.configs.VolcanoConfig attribute)

y_thresh_line_width (bioviz.configs.VolcanoConfig attribute) ylab (bioviz.configs.KMPlotConfig attribute) ylabel (bioviz.configs.KMPlotConfig attribute) ylim (bioviz.configs.KMPlotConfig attribute) (bioviz.configs.VolcanoConfig attribute) ytick_fontsize (bioviz.configs.ForestPlotConfig attribute) yticklabel_xoffset (bioviz.configs.OncoplotConfig attribute) yticks (bioviz.configs.VolcanoConfig attribute)