seismicrna.graph package

Submodules

class seismicrna.graph.abundance.ClusterAbundanceGraph(*, table: Table | PositionTable | AbundanceTable, **kwargs)

Bases: OneTableGraph

Abundance of each cluster.

property col_tracks

property data: Data of the graph.

property details: Additional details about the graph.

get_traces(): Data traces of the graph.

classmethod graph_kind(): Kind of graph.

property path_subject: Subject of the graph.

property predicate: Predicate of the graph.

property row_tracks

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.abundance.ClusterAbundanceRunner

Bases: OneTableRunner, AbundanceTableRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.abundance.ClusterAbundanceWriter(table: Table, **kwargs)

Bases: OneTableWriter

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

iter_graphs(**kwargs): Yield every graph.

class seismicrna.graph.aucroll.RollingAUCGraph(*, struct_file: Path | None, struct_reg: str | None, terminal_pairs: bool, branch: str, **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, PositionTableRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.aucroll.RollingAUCWriter(table: Table, **kwargs)

Bases: StructOneTableWriter, TableWriter

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

class seismicrna.graph.base.Annotation(row: int, col: int, x: float, y: float, text: str, **kwargs)

Bases: object

Text annotation in a graph.

class seismicrna.graph.base.BaseGraph

Bases: ABC

Base class for all types of graphs.

property annotations: list[Annotation]: Text annotations for the figure.

abstract property branches: dict[str, str]: Branches of the workflow.

property data: DataFrame: Data of the graph.

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.

abstractmethod 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.

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

abstract property path_subject: str: Subject of the graph.

property predicate: list[str]: Predicate of the graph.

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

abstract property reg: str: Name of the reference region from which the data come.

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

abstract property seq: DNA: Sequence of the region 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.

abstractmethod 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.BaseRunner

Bases: ABC

abstractmethod classmethod get_input_loader() → Callable[[Iterable, Any], Generator]: Function to load input files.

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

abstractmethod classmethod get_writer_type() → type[BaseWriter]: Type of Writer.

classmethod load_input_files(input_path: Iterable[str | Path], **kwargs): Find, filter, and load all input files.

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

abstractmethod classmethod run(*args, **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.

class seismicrna.graph.base.BaseWriter

Bases: ABC

Write the proper type(s) of graph.

abstractmethod iter_graphs(*args, **kwargs) → Generator[BaseGraph, None, None]: Yield every graph.

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

seismicrna.graph.base.get_action_name(source: MutsDataset | Table)

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

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

class seismicrna.graph.cgroup.ClusterGroupGraph

Bases: BaseGraph, ABC

Graph in which clusters can be placed in subplots.

property col_titles: Titles of the columns.

abstract property col_tracks: list[tuple[int, int]] | None: Track for each column of subplots.

property ncols: Number of columns of subplots.

property nrows: Number of rows of subplots.

property row_titles: Titles of the rows.

abstract property row_tracks: list[tuple[int, int]] | None: Track for each row of subplots.

class seismicrna.graph.cgroup.ClusterGroupRunner

Bases: BaseRunner, ABC

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

seismicrna.graph.cgroup.cgroup_table(source: Dataset | Table, cgroup: str)

seismicrna.graph.cgroup.get_ks(source: Dataset | Table): List the numbers of clusters for a source of data.

seismicrna.graph.cgroup.get_ks_clusts(source: Dataset | Table): List the clusters for a source of data.

seismicrna.graph.cgroup.make_tracks(source: Dataset | Table, k: int | None, clust: int | None, **kwargs): Make an index for the rows or columns of a graph.

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

Bases: ABC

Color map for a graph.

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

abstractmethod get_default_color() → str: Default color.

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

Bases: BaseGraph, ABC

Graph with an explicit color map.

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

abstractmethod 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, x: str)

Bases: ColorMap

Color map for relationships.

get_default_color(): Default color.

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.

get_default_color(): Default color.

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: TwoTableMergedClusterGroupGraph, OneRelGraph, 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: TwoTableRelClusterGroupRunner, RollingRunner, PositionTableRunner

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

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.corroll.RollingCorrelationWriter(table1: Table, table2: Table, **kwargs)

Bases: TwoTableRelClusterGroupWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.dataset.DatasetGraph(*, dataset: MutsDataset, num_cpus: int, **kwargs)

Bases: OneRelGraph, OneSourceClusterGroupGraph, ABC

Graph based on one Dataset.

property action: Action that generated the data.

property branches: Branches of the workflow.

property details: Additional details about the graph.

property path_subject: Subject of the graph.

property pattern: Relationship pattern for the graph.

property predicate: Predicate of the graph.

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

property reg: Name of the reference region from which the data come.

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

property seq: Sequence of the region 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.dataset.DatasetRunner

Bases: RelRunner, ClusterGroupRunner, ABC

classmethod get_input_loader(): Function to load input files.

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

abstractmethod classmethod get_writer_type() → type[DatasetWriter]: Type of Writer.

classmethod run(input_path: Iterable[str | Path], *, verify_times: bool, num_cpus: int, **kwargs): Run graphing.

class seismicrna.graph.dataset.DatasetWriter(*, dataset: MutsDataset, **kwargs)

Bases: BaseWriter, ABC

abstractmethod get_graph(*args, **kwargs) → DatasetGraph: Return a graph instance.

iter_graphs(*, rels: list[str], cgroup: str, **kwargs): Yield every graph.

class seismicrna.graph.delprof.DeltaProfileGraph(*, k1: int | None, clust1: int | None, k2: int | None, clust2: int | None, **kwargs)

Bases: TwoTableMergedClusterGroupGraph, OneRelGraph, 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: TwoTableRelClusterGroupRunner, PositionTableRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.delprof.DeltaProfileWriter(table1: Table, table2: Table, **kwargs)

Bases: TwoTableRelClusterGroupWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.giniroll.RollingGiniGraph(*, table: Table | PositionTable | AbundanceTable, **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 Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.giniroll.RollingGiniWriter(table: Table, **kwargs)

Bases: RollingStatWriter

classmethod get_graph_type(): Type of graph.

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

Bases: OneTableRelClusterGroupGraph, 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).

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

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

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

get_traces(): Data traces of the graph.

property x_title: Title of the x-axis.

class seismicrna.graph.hist.HistogramRunner

Bases: OneTableRelClusterGroupRunner, ABC

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

class seismicrna.graph.hist.HistogramWriter(table: Table, **kwargs)

Bases: OneTableRelClusterGroupWriter, ABC

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

abstractmethod classmethod get_graph_type() → type[HistogramGraph]: Type of graph.

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.PositionHistogramGraph(*, hist_bins: int, hist_margin: float, **kwargs)

Bases: HistogramGraph

classmethod graph_kind(): Kind of graph.

classmethod what(): What is being graphed.

property y_title: Title of the y-axis.

class seismicrna.graph.histpos.PositionHistogramRunner

Bases: HistogramRunner, PositionTableRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.histpos.PositionHistogramWriter(table: Table, **kwargs)

Bases: HistogramWriter, TableWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.histread.ReadHistogramGraph(*, hist_bins: int, hist_margin: float, **kwargs)

Bases: HistogramGraph

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: HistogramRunner, ReadTableRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.histread.ReadHistogramWriter(table: Table, **kwargs)

Bases: HistogramWriter, TableWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.mutdist.MutationDistanceGraph(*, mutdist_null: bool, **kwargs)

Bases: DatasetGraph, ColorMapGraph

Distance between the closest two mutations in each read.

property data: Data of the graph.

property g_test: G-test statistic and P-value.

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

get_traces(): Data traces of the graph.

classmethod graph_kind(): Kind of graph.

property hists

property loc_clusters

property max_read_length

property row_tracks: Track for each row of subplots.

property table

property tabulator

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.mutdist.MutationDistanceRunner

Bases: DatasetRunner

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

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.mutdist.MutationDistanceWriter(*, dataset: MutsDataset, **kwargs)

Bases: DatasetWriter

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

seismicrna.graph.mutdist.get_null_name(name: str)

class seismicrna.graph.onesource.OneSourceClusterGroupGraph(*, k: int | None, clust: int | None, **kwargs)

Bases: OneSourceGraph, ClusterGroupGraph, ABC

property path_subject: Subject of the graph.

class seismicrna.graph.onesource.OneSourceGraph

Bases: BaseGraph, ABC

Graph of data from one source of data (Dataset or Table).

property action: str: Action that generated the data.

property col_tracks

property title_action_sample: Action and sample for the title.

class seismicrna.graph.onestruct.StructOneTableGraph(*, struct_file: Path | None, struct_reg: str | None, terminal_pairs: bool, branch: str, **kwargs)

Bases: OneTableRelClusterGroupGraph, OneRelGraph, ABC

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

property branches: Branches of the workflow.

property details: Additional details about the graph.

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 predicate: Predicate of the graph.

property struct_reg: Name of the region from which the structure comes.

class seismicrna.graph.onestruct.StructOneTableRunner

Bases: OneTableRelClusterGroupRunner, ABC

classmethod get_input_loader(): Function to load input files.

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

class seismicrna.graph.onestruct.StructOneTableWriter(table: Table, **kwargs)

Bases: OneTableRelClusterGroupWriter, ABC

iter_graphs(*, rels: list[str], cgroup: str, struct_file: Iterable[str | Path] = (), fold_coords: Iterable[tuple[str, int, int]] = (), fold_primers: Iterable[tuple[str, DNA, DNA]] = (), fold_regions_file: str | None = None, fold_full: bool = True, **kwargs): Yield every graph.

class seismicrna.graph.onetable.OneTableGraph(*, table: Table | PositionTable | AbundanceTable, **kwargs)

Bases: TableGraph, OneSourceGraph, ABC

Graph of data from one Table.

property action: Action that generated the data.

property branches: Branches of the workflow.

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

property reg: Name of the reference region from which the data come.

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

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

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

class seismicrna.graph.onetable.OneTableRelClusterGroupGraph(*, table: Table | PositionTable | AbundanceTable, **kwargs)

Bases: OneTableGraph, RelTableGraph, OneSourceClusterGroupGraph, ABC

property row_tracks: Track for each row of subplots.

class seismicrna.graph.onetable.OneTableRelClusterGroupRunner: Bases: OneTableRunner, RelTableRunner, ClusterGroupRunner, ABC

class seismicrna.graph.onetable.OneTableRelClusterGroupWriter(table: Table, **kwargs)

Bases: OneTableWriter, ABC

iter_graphs(*, rels: list[str], cgroup: str, **kwargs): Yield every graph.

class seismicrna.graph.onetable.OneTableRunner

Bases: TableRunner, ABC

classmethod run(input_path: Iterable[str | Path], *, verify_times: bool, num_cpus: int, **kwargs): Run graphing.

class seismicrna.graph.onetable.OneTableWriter(table: Table, **kwargs)

Bases: TableWriter, ABC

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

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

class seismicrna.graph.poscorr.PositionCorrelationGraph(*, dataset: MutsDataset, num_cpus: int, **kwargs)

Bases: PositionPairGraph, ABC

Phi correlations between pairs of positions.

classmethod get_pair_func(): Function to compare each pair of positions.

classmethod graph_kind(): Kind of graph.

classmethod what(): What is being graphed.

class seismicrna.graph.poscorr.PositionCorrelationRunner

Bases: PositionPairRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.poscorr.PositionCorrelationWriter(*, dataset: MutsDataset, **kwargs)

Bases: PositionPairWriter

classmethod graph_type(): Type of graph.

Calculate the phi correlation coefficient for a 2x2 matrix.

.B .O ..

where: A. = AB + AO .B = AB + OB .. = A. + O. = .B + .O

Parameters:

n (int | float | np.ndarray | pd.Series) – Observations in total (..)
a (int | float | np.ndarray | pd.Series | pd.DataFrame) – Observations for which A is true, regardless of B (A.)
b (int | float | np.ndarray | pd.Series | pd.DataFrame) – Observations for which B is true, regardless of A (.B)
a_and_b (int | float | np.ndarray | pd.Series | pd.DataFrame) – Observations for which A and B are both true (AB)

Returns:

Phi correlation coefficient

Return type:

float | np.ndarray | pd.Series | pd.DataFrame

class seismicrna.graph.pospair.PositionPairGraph(*, dataset: MutsDataset, num_cpus: int, **kwargs)

Bases: DatasetGraph, ABC

Function of pairs of positions.

property data: Data of the graph.

abstractmethod classmethod get_pair_func(): Function to compare each pair of positions.

get_traces(): Data traces of the graph.

property row_tracks: Track for each row of subplots.

property x_title: Title of the x-axis.

property y_title: Title of the y-axis.

class seismicrna.graph.pospair.PositionPairRunner

Bases: DatasetRunner, ABC

abstractmethod classmethod get_writer_type() → type[PositionPairWriter]: Type of Writer.

class seismicrna.graph.pospair.PositionPairWriter(*, dataset: MutsDataset, **kwargs)

Bases: DatasetWriter

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

abstractmethod classmethod graph_type(): Type of graph.

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 | PositionTable | AbundanceTable, **kwargs)

Bases: OneTableRelClusterGroupGraph, 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: OneTableRelClusterGroupRunner, PositionTableRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.profile.ProfileWriter(table: Table, **kwargs)

Bases: OneTableRelClusterGroupWriter

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

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

Bases: RelGraph, 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: RelGraph, 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.rel.RelGraph

Bases: BaseGraph, ABC

Graph of one or more types of relationships.

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

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

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

class seismicrna.graph.rel.RelRunner

Bases: BaseRunner, ABC

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

class seismicrna.graph.roc.ROCGraph(*, struct_file: Path | None, struct_reg: str | None, terminal_pairs: bool, branch: str, **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, PositionTableRunner

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.roc.ROCWriter(table: Table, **kwargs)

Bases: StructOneTableWriter, TableWriter

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: TableGraph, 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: TableRunner, ABC

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

class seismicrna.graph.scatter.ScatterGraph(*, metric: str, **kwargs)

Bases: TwoTableRelClusterGroupGraph, OneRelGraph, ColorMapGraph

property annotations: Text annotations for the figure.

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 xmax

property y_title: Title of the y-axis.

property ymax

class seismicrna.graph.scatter.ScatterRunner

Bases: TwoTableRelClusterGroupRunner, PositionTableRunner

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

classmethod get_writer_type(): Type of Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.scatter.ScatterWriter(table1: Table, table2: Table, **kwargs)

Bases: TwoTableRelClusterGroupWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.snrroll.RollingSNRGraph(*, table: Table | PositionTable | AbundanceTable, **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 Writer.

classmethod run(*args, **kwargs): Run graphing.

class seismicrna.graph.snrroll.RollingSNRWriter(table: Table, **kwargs)

Bases: RollingStatWriter

classmethod get_graph_type(): Type of graph.

class seismicrna.graph.statroll.RollingStatGraph(*, table: Table | PositionTable | AbundanceTable, **kwargs)

Bases: OneTableRelClusterGroupGraph, OneRelGraph, RollingGraph, ABC

property data: Data of the graph.

get_traces(): Data traces of the graph.

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

class seismicrna.graph.statroll.RollingStatRunner: Bases: OneTableRelClusterGroupRunner, RollingRunner, PositionTableRunner, ABC

class seismicrna.graph.statroll.RollingStatWriter(table: Table, **kwargs)

Bases: OneTableRelClusterGroupWriter, TableWriter, ABC

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

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

class seismicrna.graph.table.AbundanceTableRunner

Bases: TableRunner, ABC

classmethod get_input_loader(): Function to load input files.

class seismicrna.graph.table.PositionTableRunner

Bases: RelTableRunner, ABC

classmethod get_input_loader(): Function to load input files.

class seismicrna.graph.table.ReadTableRunner

Bases: RelTableRunner, ABC

classmethod get_input_loader(): Function to load input files.

class seismicrna.graph.table.RelTableGraph(*, use_ratio: bool, **kwargs)

Bases: TableGraph, RelGraph, ABC

property predicate: Predicate of the graph.

class seismicrna.graph.table.RelTableRunner: Bases: RelRunner, TableRunner, ABC

class seismicrna.graph.table.TableGraph(*, use_ratio: bool, **kwargs)

Bases: BaseGraph, ABC

Graph based on one or more tables.

property data_kind

either “ratio” or “count”.

Type:: Kind of data being used

class seismicrna.graph.table.TableRunner

Bases: BaseRunner, ABC

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

abstractmethod classmethod get_writer_type() → type[TableWriter]: Type of Writer.

class seismicrna.graph.table.TableWriter(*tables: Table, **kwargs)

Bases: BaseWriter, ABC

abstractmethod iter_graphs(*args, **kwargs) → Generator[TableGraph, None, None]: Yield every graph.

seismicrna.graph.table.load_abundance_tables(input_paths: Iterable[str | Path], **kwargs): Load read tables.

seismicrna.graph.table.load_pos_tables(input_paths: Iterable[str | Path], **kwargs): Load position tables.

seismicrna.graph.table.load_read_tables(input_paths: Iterable[str | Path], **kwargs): Load read tables.

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_pairwise_position_trace(data: Series, end5: int, end3: int)

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)

seismicrna.graph.trace.iter_stack_bar_traces(data: DataFrame)

class seismicrna.graph.twotable.TwoTableGraph(*, out_dir: str | Path, table1: Table | PositionTable, table2: Table | PositionTable, **kwargs)

Bases: TableGraph, 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 branches: Branches of the workflow.

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

property reg: Name of the reference region from which the data come.

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 seq: Sequence of the region 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.twotable.TwoTableMergedClusterGroupGraph(*, k1: int | None, clust1: int | None, k2: int | None, clust2: int | None, **kwargs)

Bases: TwoTableRelClusterGroupGraph, 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.TwoTableRelClusterGroupGraph(*, k1: int | None, clust1: int | None, k2: int | None, clust2: int | None, **kwargs)

Bases: TwoTableGraph, RelTableGraph, ClusterGroupGraph, ABC

property col_tracks: Track for each column 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 row_tracks: Track for each row of subplots.

class seismicrna.graph.twotable.TwoTableRelClusterGroupRunner: Bases: TwoTableRunner, RelTableRunner, ClusterGroupRunner, ABC

class seismicrna.graph.twotable.TwoTableRelClusterGroupWriter(table1: Table, table2: Table, **kwargs)

Bases: TwoTableWriter, ABC

iter_graphs(*, rels: list[str], cgroup: str, **kwargs): Yield every graph.

class seismicrna.graph.twotable.TwoTableRunner

Bases: TableRunner, ABC

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

abstractmethod classmethod get_writer_type() → type[TwoTableWriter]: Type of Writer.

classmethod run(input_path: Iterable[str | Path], *, compself: bool, comppair: bool, verify_times: bool, num_cpus: int, **kwargs): Run graphing.

class seismicrna.graph.twotable.TwoTableWriter(table1: Table, table2: Table, **kwargs)

Bases: TableWriter, ABC

Write the proper types of graphs for two given tables.

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

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_table_pairs(tables: Iterable[Table]): Yield every pair of tables whose reference and region match.