Types

Types used throughout polyflame

class polyflame.types.PlotInfo

Dictionary passed to plotting functions

colorSequential: str

Palette name to use for sequential colors

colors: list[str]

Color palette to use, must be a list of valid RGB color hex codes, with an appropriate length

cols: dict[str, str]

Column mappings from the column types expected to the actual column names in data

title: str

Title of plot

xlabel: str

Label for x-axis

ylabel: str

Label for y-axis

class polyflame.types.DataPlotInfo

Extension of polyflame.types.PlotInfo to add data and plot type

data: DataFrame

Data corresponding to the plot

type: Literal['pyramid', 'upset', 'proportion'] | None

Type of plot

class polyflame.types.SourceInfo

Source information for analysis functions to load data

N: int | None

Number of patients

checksum: str

Data integrity checksum

checksum_file: str

File for which data integrity checksum is calculated

path: Path

Path where source is located

class polyflame.types.ReadableTermColumnInfo

Dictionary type defining the mapping from term columns to readable names in a taxonomy

drop_nulls: bool

Whether rows containing nulls (after mapping) should be dropped from the data, by default, rows are not dropped

taxonomy_section: str

Section in taxonomy file that should be used for mapping. If not given, this is taken to be the same as term_column

term_column: Required[str]

Column in data that should be mapped from codes to readable names