seismicrna.graph package

Submodules

class seismicrna.graph.aucroll.RollingAUCGraph(*, struct_file: Path | None, struct_sect: str | None, **kwargs)

Bases: StructOneTableGraph, RollingGraph

property data: Data of the graph.

get_traces(): Data traces of the graph.

classmethod graph_kind(): Kind of graph.

property profile_names: Names of the profiles as they appear in the data.

classmethod what(): What is being graphed.

property y_title: Title of the y-axis.

class seismicrna.graph.aucroll.RollingAUCRunner

Bases: RollingRunner, StructOneTableRunner, PosGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.aucroll.RollingAUCWriter(table_file: Path)

Bases: StructOneTableWriter, PosGraphWriter

get_graph(rels_group: str, **kwargs): Return a graph instance.

class seismicrna.graph.base.GraphBase(*, use_ratio: bool, quantile: float)

Bases: ABC

abstract property codestring: String of the relationship code(s).

abstract property col_index: Index | None: Index of columns of subplots.

property col_titles: Titles of the columns.

property data: DataFrame: Data of the graph.

property data_kind

either “ratio” or “count”.

Type:: Kind of data being used

property details: list[str]: Additional details about the graph.

property figure: Figure object.

get_path(ext: str): Path to the output file of the graph.

get_path_fields(): Path fields.

classmethod get_path_segs(): Path segments.

abstract get_traces() → Iterable[tuple[tuple[int, int], Trace]]: Data traces of the graph.

property graph_filename: Name of the graph’s output file, without its extension.

abstract classmethod graph_kind() → str: Kind of graph.

property ncols: Number of columns of subplots.

property nrows: Number of rows of subplots.

abstract property path_subject: Subject of the graph.

property predicate: Predicate of the graph.

abstract property ref: str: Name of the reference sequence from which the data come.

abstract property rel_names: Names of the relationships to graph.

property relationships: str: Relationships being graphed as a slash-separated string.

abstract property row_index: Index | None: Index of rows of subplots.

property row_titles: Titles of the rows.

abstract property sample: str: Name(s) of the sample(s) from which the data come.

abstract property sect: str: Name of the reference section from which the data come.

abstract property seq: DNA: Sequence of the section from which the data come.

property title: Title of the graph.

abstract property title_action_sample: str: Action and sample for the title.

abstract property top: Path: Path of the top-level output directory for all files.

abstract classmethod what() → str: What is being graphed.

write(csv: bool, html: bool, svg: bool, pdf: bool, png: bool, force: bool = False): Write the selected files.

write_csv(force: bool): Write the graph’s source data to a CSV file.

write_html(force: bool): Write the graph to an HTML file.

write_pdf(force: bool): Write the graph to a PDF file.

write_png(force: bool): Write the graph to a PNG file.

write_svg(force: bool): Write the graph to an SVG file.

abstract property x_title: str: Title of the x-axis.

abstract property y_title: str: Title of the y-axis.

class seismicrna.graph.base.GraphRunner

Bases: ABC

abstract classmethod get_table_finder() → Callable[[tuple[str, ...]], Generator]: Function to find and filter table files.

abstract classmethod get_writer_type() → type[GraphWriter]: Type of GraphWriter.

classmethod list_table_files(input_path: tuple[str, ...]): Find, filter, and list all table files from input files.

classmethod params() → list[Argument | Option]: Parameters for the command line.

abstract classmethod run(input_path: tuple[str, ...], *, rels: tuple[str, ...], use_ratio: bool, quantile: float, cgroup: str, csv: bool, html: bool, svg: bool, pdf: bool, png: bool, force: bool, max_procs: int, parallel: bool, **kwargs) → list[Path]: Run graphing.

classmethod universal_input_params(): Universal parameters controlling the input data.

classmethod universal_output_params(): Universal parameters controlling the output graph.

classmethod var_params() → list[Argument | Option]: Parameters that can vary among different classes.

class seismicrna.graph.base.GraphWriter(*table_files: Path)

Bases: ABC

Write the proper graph(s) for the table(s).

abstract classmethod get_table_loader() → Callable[[Path], Table]: Function to load table files.

abstract iter_graphs(*args, **kwargs) → Generator[GraphBase, None, None]: Yield every graph for the table.

classmethod load_table_file(table_file: Path): Load one table file.

write(*args, csv: bool, html: bool, svg: bool, pdf: bool, png: bool, force: bool, **kwargs): Generate and write every graph for the table.

class seismicrna.graph.base.PosGraphRunner

Bases: GraphRunner, ABC

classmethod get_table_finder(): Function to find and filter table files.

class seismicrna.graph.base.PosGraphWriter(*table_files: Path)

Bases: GraphWriter, ABC

classmethod get_table_loader(): Function to load table files.

class seismicrna.graph.base.ReadGraphRunner

Bases: GraphRunner, ABC

classmethod get_table_finder(): Function to find and filter table files.

class seismicrna.graph.base.ReadGraphWriter(*table_files: Path)

Bases: GraphWriter, ABC

classmethod get_table_loader(): Function to load table files.

seismicrna.graph.base.cgroup_table(table: Table, cgroup: str)

seismicrna.graph.base.get_action_name(table: Table)

seismicrna.graph.base.make_index(header: Header, order: int | None, clust: int | None): Make an index for the rows or columns of a graph.

seismicrna.graph.base.make_path_subject(action: str, order: int | None, clust: int | None)

seismicrna.graph.base.make_title_action_sample(action: str, sample: str)

class seismicrna.graph.color.ColorMap(name: str, **kwargs)

Bases: ABC

Color map for a graph.

get(item: Hashable, default: Any | None = None)

class seismicrna.graph.color.ColorMapGraph(*, cmap: str | None = None, **kwargs)

Bases: GraphBase, ABC

Graph with an explicit color map.

property cmap: ColorMap: Color map of the graph.

abstract classmethod get_cmap_type() → type[ColorMap]: Type of the color map.

class seismicrna.graph.color.RelColorMap(name: str, v: str, n: str, e: str, m: str, d: str, i: str, s: str, a: str, c: str, g: str, t: str)

Bases: ColorMap

Color map for relationships.

class seismicrna.graph.color.SeqColorMap(name: str, a: str, c: str, g: str, t: str, n: str)

Bases: ColorMap

Color map for bases A, C, G, and T.

seismicrna.graph.color.get_cmap(cmap_class: type[ColorMap], name: str | None = None): Get a color map of a given class by its name.

seismicrna.graph.color.get_colormaps(cmap_class: type[ColorMap]): Return a dict of all color maps of a given class.

class seismicrna.graph.corroll.RollingCorrelationGraph(*, metric: str, **kwargs)

Bases: TwoTableMergedGraph, RollingGraph

property details: Additional details about the graph.

classmethod graph_kind(): Kind of graph.

property predicate: Predicate of the graph.

classmethod what(): What is being graphed.

property y_title: Title of the y-axis.

class seismicrna.graph.corroll.RollingCorrelationRunner

Bases: RollingRunner, TwoTableRunner, PosGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

classmethod var_params(): Parameters that can vary among different classes.

class seismicrna.graph.corroll.RollingCorrelationWriter(table1_file: Path, table2_file: Path)

Bases: TwoTableWriter, PosGraphWriter

classmethod get_graph_type(): Type of graph.

Bases: TwoTableMergedGraph, ColorMapGraph

classmethod get_cmap_type(): Type of the color map.

classmethod graph_kind(): Kind of graph.

classmethod what(): What is being graphed.

property x_title: str: Title of the x-axis.

property y_title: Title of the y-axis.

class seismicrna.graph.delprof.DeltaProfileRunner

Bases: TwoTableRunner, PosGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.delprof.DeltaProfileWriter(table1_file: Path, table2_file: Path)

Bases: TwoTableWriter, PosGraphWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.giniroll.RollingGiniGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: RollingStatGraph

classmethod graph_kind(): Kind of graph.

classmethod stat_func(): Function to compute a statistic on the data.

classmethod what(): What is being graphed.

property y_title: Title of the y-axis.

class seismicrna.graph.giniroll.RollingGiniRunner

Bases: RollingStatRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.giniroll.RollingGiniWriter(table_file: Path)

Bases: RollingStatWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.hist.HistogramGraph(*, hist_bins: int, hist_margin: float, **kwargs)

Bases: GraphBase, ABC

Generic histogram.

get_bounds(data: DataFrame): Get the lower and upper bounds of the histogram.

get_edges(data: DataFrame): Get the edges of the histogram bins.

class seismicrna.graph.hist.HistogramRunner

Bases: GraphRunner, ABC

classmethod var_params(): Parameters that can vary among different classes.

seismicrna.graph.hist.get_edges_index(edges: ndarray, use_ratio: bool)

Generate an index for the edges of histogram bins.

Parameters:

edges (numpy.ndarray) – Edges of histogram bins.
use_ratio (bool) – Assume the edges represent ratios rather than counts.

Returns:

Index for the edges.

Return type:

pandas.Index | pandas.MultiIndex

class seismicrna.graph.histpos.PosHistogramGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: RelHistogramGraph

classmethod graph_kind(): Kind of graph.

classmethod what(): What is being graphed.

property y_title: Title of the y-axis.

class seismicrna.graph.histpos.PosHistogramRunner

Bases: RelHistogramRunner, PosGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.histpos.PosHistogramWriter(table_file: Path)

Bases: RelHistogramWriter, PosGraphWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.histread.ReadHistogramGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: RelHistogramGraph

classmethod graph_kind(): Kind of graph.

classmethod what(): What is being graphed.

property y_title: Title of the y-axis.

class seismicrna.graph.histread.ReadHistogramRunner

Bases: RelHistogramRunner, ReadGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.histread.ReadHistogramWriter(table_file: Path)

Bases: RelHistogramWriter, ReadGraphWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.histrel.RelHistogramGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: OneTableGraph, HistogramGraph, MultiRelsGraph, ColorMapGraph, ABC

Histogram of relationship(s) in one table.

property data: Data of the graph.

property data_header: Header of the selected data (not of the entire table).

classmethod get_cmap_type(): Type of the color map.

get_traces(): Data traces of the graph.

property x_title: Title of the x-axis.

class seismicrna.graph.histrel.RelHistogramRunner: Bases: OneTableRunner, HistogramRunner, ABC

class seismicrna.graph.histrel.RelHistogramWriter(table_file: Path)

Bases: OneTableWriter, ABC

get_graph(rels_group: str, **kwargs): Return a graph instance.

abstract classmethod get_graph_type() → type[RelHistogramGraph]: Type of graph.

class seismicrna.graph.onestruct.StructOneTableGraph(*, struct_file: Path | None, struct_sect: str | None, **kwargs)

Bases: OneTableGraph, OneRelGraph, ABC

Graph of data from one Table applied to RNA structure(s).

get_path_fields(): Path fields.

iter_profiles(): Yield each RNAProfile from the table.

iter_states(): Yield each RNAState.

property path_subject: Subject of the graph.

property struct_sect: Name of the section from which the structure comes.

class seismicrna.graph.onestruct.StructOneTableRunner

Bases: OneTableRunner, ABC

classmethod get_table_finder(): Function to find and filter table files.

classmethod var_params(): Parameters that can vary among different classes.

class seismicrna.graph.onestruct.StructOneTableWriter(table_file: Path)

Bases: OneTableWriter, ABC

iter_graphs(rels: tuple[str, ...], cgroup: str, struct_file: tuple[str, ...] = (), fold_coords: tuple[tuple[str, int, int], ...] = (), fold_primers: tuple[tuple[str, DNA, DNA], ...] = (), fold_sections_file: str | None = None, fold_full: bool = True, **kwargs): Yield every graph for the table.

class seismicrna.graph.onetable.OneTableGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: GraphBase, ABC

Graph of data from one Table.

property action: Action that generated the data.

property col_index: Index of columns of subplots.

property path_subject: Subject of the graph.

property ref: Name of the reference sequence from which the data come.

property row_index: Index of rows of subplots.

property sample: Name(s) of the sample(s) from which the data come.

property sect: Name of the reference section from which the data come.

property seq: Sequence of the section from which the data come.

property title_action_sample: Action and sample for the title.

property top: Path of the top-level output directory for all files.

class seismicrna.graph.onetable.OneTableRunner

Bases: GraphRunner, ABC

classmethod run(input_path: tuple[str, ...], *, max_procs: int, parallel: bool, **kwargs): Run graphing.

class seismicrna.graph.onetable.OneTableWriter(table_file: Path)

Bases: GraphWriter, ABC

abstract get_graph(*args, **kwargs) → OneTableGraph: Return a graph instance.

iter_graphs(rels: tuple[str, ...], cgroup: str, **kwargs): Yield every graph for the table.

property table: The table providing the data for the graph(s).

class seismicrna.graph.profile.MultiRelsProfileGraph(*, rels: str, **kwargs)

Bases: MultiRelsGraph, ProfileGraph

Stacked bar graph with multiple relationships per position.

classmethod get_cmap_type(): Type of the color map.

get_traces(): Data traces of the graph.

classmethod what(): What is being graphed.

class seismicrna.graph.profile.OneRelProfileGraph(*, rel: str, **kwargs)

Bases: OneRelGraph, ProfileGraph

Bar graph with one relationship per position.

classmethod get_cmap_type(): Type of the color map.

get_traces(): Data traces of the graph.

classmethod what(): What is being graphed.

class seismicrna.graph.profile.ProfileGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: OneTableGraph, ColorMapGraph, ABC

Bar graph of a mutational profile for one table.

property data: Data of the graph.

property data_header: Header of the selected data (not of the entire table).

classmethod graph_kind(): Kind of graph.

property x_title: Title of the x-axis.

property y_title: Title of the y-axis.

class seismicrna.graph.profile.ProfileRunner

Bases: OneTableRunner, PosGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.profile.ProfileWriter(table_file: Path)

Bases: OneTableWriter, PosGraphWriter

get_graph(rels_group: str, **kwargs): Return a graph instance.

class seismicrna.graph.rel.MultiRelsGraph(*, rels: str, **kwargs)

Bases: GraphBase, ABC

Graph of one or more relationships.

property codestring: String of the relationship code(s).

property rel_names: Names of the relationships to graph.

class seismicrna.graph.rel.OneRelGraph(*, rel: str, **kwargs)

Bases: GraphBase, ABC

Graph of exactly one type of relationship.

property codestring: String of the relationship code(s).

property rel_name: Name of the relationship to graph.

property rel_names: Names of the relationships to graph.

class seismicrna.graph.roc.ROCGraph(*, struct_file: Path | None, struct_sect: str | None, **kwargs)

Bases: StructOneTableGraph

Graph of a receiver operating characteristic (ROC) curve.

property data: Data of the graph.

property fpr: False positive rate (FPR) of each RNA state.

get_traces(): Data traces of the graph.

classmethod graph_kind(): Kind of graph.

property profile_names: Names of the profiles as they appear in the data.

property tpr: True positive rate (TPR) of each RNA state.

classmethod what(): What is being graphed.

property x_title: Title of the x-axis.

property y_title: Title of the y-axis.

class seismicrna.graph.roc.ROCRunner

Bases: StructOneTableRunner, PosGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.roc.ROCWriter(table_file: Path)

Bases: StructOneTableWriter, PosGraphWriter

get_graph(rels_group: str, **kwargs): Return a graph instance.

seismicrna.graph.roc.rename_columns(df: DataFrame): Rename the levels of the columns.

class seismicrna.graph.roll.RollingGraph(*, window: int, winmin: int, **kwargs)

Bases: GraphBase, ABC

property details: Additional details about the graph.

property predicate: Predicate of the graph.

property x_title: Title of the x-axis.

class seismicrna.graph.roll.RollingRunner

Bases: GraphRunner, ABC

classmethod var_params(): Parameters that can vary among different classes.

Bases: TwoTableGraph, ColorMapGraph

property data: Data of the graph.

classmethod get_cmap_type(): Type of the color map.

get_traces(): Data traces of the graph.

classmethod graph_kind(): Kind of graph.

classmethod what(): What is being graphed.

property x_title: Title of the x-axis.

property y_title: Title of the y-axis.

class seismicrna.graph.scatter.ScatterPlotRunner

Bases: TwoTableRunner, PosGraphRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.scatter.ScatterPlotWriter(table1_file: Path, table2_file: Path)

Bases: TwoTableWriter, PosGraphWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.snrroll.RollingSNRGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: RollingStatGraph

classmethod graph_kind(): Kind of graph.

classmethod stat_func(): Function to compute a statistic on the data.

classmethod what(): What is being graphed.

property y_title: Title of the y-axis.

class seismicrna.graph.snrroll.RollingSNRRunner

Bases: RollingStatRunner

classmethod get_writer_type(): Type of GraphWriter.

class seismicrna.graph.snrroll.RollingSNRWriter(table_file: Path)

Bases: RollingStatWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.statroll.RollingStatGraph(*, table: Table | PosTable, order: int | None, clust: int | None, **kwargs)

Bases: OneTableGraph, OneRelGraph, RollingGraph, ABC

property data: Data of the graph.

get_traces(): Data traces of the graph.

abstract classmethod stat_func() → Callable[[Series], Series]: Function to compute a statistic on the data.

class seismicrna.graph.statroll.RollingStatRunner: Bases: RollingRunner, OneTableRunner, PosGraphRunner, ABC

class seismicrna.graph.statroll.RollingStatWriter(table_file: Path)

Bases: OneTableWriter, PosGraphWriter, ABC

get_graph(rels_group: str, **kwargs): Return a graph instance.

abstract classmethod get_graph_type() → type[RollingGraph]: Type of graph.

seismicrna.graph.trace.get_hist_trace(data: Series, rel: str, cmap: ColorMap)

seismicrna.graph.trace.get_line_trace(gini: Series, cluster: str)

seismicrna.graph.trace.get_roc_trace(fpr: Series, tpr: Series, profile: str, struct: str)

seismicrna.graph.trace.get_rolling_auc_trace(auc: Series, profile: str, struct: str)

seismicrna.graph.trace.get_seq_base_bar_trace(data: Series, cmap: ColorMap, base: str)

seismicrna.graph.trace.get_seq_base_scatter_trace(xdata: Series, ydata: Series, cmap: ColorMap, base: str)

seismicrna.graph.trace.get_seq_line_trace(data: Series)

seismicrna.graph.trace.get_seq_stack_bar_trace(data: Series, rel: str, cmap: ColorMap)

seismicrna.graph.trace.iter_hist_traces(data: DataFrame, cmap: ColorMap)

seismicrna.graph.trace.iter_line_traces(lines: DataFrame)

seismicrna.graph.trace.iter_roc_traces(fprs: DataFrame, tprs: DataFrame, profile: str)

seismicrna.graph.trace.iter_rolling_auc_traces(aucs: DataFrame, profile: str)

seismicrna.graph.trace.iter_seq_base_bar_traces(data: Series, cmap: ColorMap)

seismicrna.graph.trace.iter_seq_base_scatter_traces(xdata: Series, ydata: Series, cmap: ColorMap)

seismicrna.graph.trace.iter_seq_line_traces(data: Series, *_, **__)

seismicrna.graph.trace.iter_seqbar_stack_traces(data: DataFrame, cmap: ColorMap)

Bases: OneRelGraph, ABC

Graph of two Tables.

property action1: Action that generated dataset 1.

property action2: Action that generated dataset 2.

property action_sample1: Action and sample of dataset 1.

property action_sample2: Action and sample of dataset 2.

property col_index: Index of columns of subplots.

property data1: Data from table 1.

property data2: Data from table 2.

property path_subject: Subject of the graph.

property path_subject1: Name of subject 1.

property path_subject2: Name of subject 2.

property ref: Name of the reference sequence from which the data come.

property row_index: Index of rows of subplots.

property sample: Name(s) of the sample(s) from which the data come.

property sample1: Name of sample 1.

property sample2: Name of sample 2.

property sect: Name of the reference section from which the data come.

property seq: Sequence of the section from which the data come.

property title_action_sample: Action and sample for the title.

property top: Path of the top-level output directory for all files.

Bases: TwoTableGraph, ABC

Graph of a pair of datasets over the same sequence in which the data series are merged in some fashion into another series, and the original data are not graphed directly.

property data: Data of the graph.

get_traces(): Data traces of the graph.

class seismicrna.graph.twotable.TwoTableRunner

Bases: GraphRunner, ABC

abstract classmethod get_writer_type() → type[TwoTableWriter]: Type of GraphWriter.

classmethod run(input_path: tuple[str, ...], *, compself: bool, comppair: bool, max_procs: int, parallel: bool, **kwargs): Run graphing.

classmethod var_params(): Parameters that can vary among different classes.

class seismicrna.graph.twotable.TwoTableWriter(table1_file: Path, table2_file: Path)

Bases: GraphWriter, ABC

Write the proper types of graphs for two given tables.

abstract classmethod get_graph_type(*args, **kwargs) → type[TwoTableGraph]: Type of graph.

iter_graphs(rels: tuple[str, ...], cgroup: str, **kwargs): Yield every graph for the table.

property table1: The first table providing the data for the graph(s).

property table2: The second table providing the data for the graph(s).

seismicrna.graph.twotable.iter_pos_table_pairs(table_files: Iterable[Path]): Yield every pair of files of positional tables whose reference and section match.

seismicrna.graph.twotable.iter_read_table_pairs(table_files: Iterable[Path]): Yield every pair of files of per-read tables whose reference and section match.