spateo.configuration

Module Contents

Classes

SpateoConfig
SpateoAdataKeyManager

Functions

shiftedColorMap(→ matplotlib.colors.ListedColormap)	Function to offset the "center" of a colormap. Useful for
reset_rcParams()	Reset matplotlib.rcParams to defaults.
spateo_theme([background])
config_spateo_rcParams(→ None)	Configure matplotlib.rcParams to spateo defaults (based on ggplot style and scanpy).
set_figure_params(, dpi, dpi_save, frameon, ...)	Set resolution/size, styling and format of figures.
set_pub_style(→ None)	formatting helper function that can be used to save publishable figures
set_pub_style_mpltex()	formatting helper function based on mpltex package that can be used to save publishable figures

Attributes

EPS
MAX
config
SKM
fire_cmap
darkblue_cmap
darkgreen_cmap
darkred_cmap
darkpurple_cmap
div_blue_black_red_cmap
div_blue_red_cmap
glasbey_white_cmap
glasbey_dark_cmap
_themes
zebrafish_colors
cyc_10
cyc_20
zebrafish_256

spateo.configuration.EPS

spateo.configuration.MAX

class spateo.configuration.SpateoConfig(logging_level: int = logging.INFO, n_threads: int = os.cpu_count())

property logging_level

property n_threads

spateo.configuration.config

class spateo.configuration.SpateoAdataKeyManager

ADATA_TYPE_KEY = '__type'

ADATA_DEFAULT_TYPE

ADATA_AGG_TYPE = 'AGG'

ADATA_UMI_TYPE = 'UMI'

UNS_PP_KEY = 'pp'

UNS_SPATIAL_KEY = 'spatial'

UNS_SPATIAL_BINSIZE_KEY = 'binsize'

UNS_SPATIAL_SCALE_KEY = 'scale'

UNS_SPATIAL_SCALE_UNIT_KEY = 'scale_unit'

UNS_SPATIAL_SEGMENTATION_KEY = 'segmentation'

UNS_SPATIAL_ALIGNMENT_KEY = 'alignment'

UNS_SPATIAL_QC_KEY = 'qc'

SPLICED_LAYER_KEY = 'spliced'

UNSPLICED_LAYER_KEY = 'unspliced'

STAIN_LAYER_KEY = 'stain'

LABELS_LAYER_KEY = 'labels'

MASK_SUFFIX = 'mask'

MARKERS_SUFFIX = 'markers'

DISTANCES_SUFFIX = 'distances'

BINS_SUFFIX = 'bins'

LABELS_SUFFIX = 'labels'

SCORES_SUFFIX = 'scores'

EXPANDED_SUFFIX = 'expanded'

AUGMENTED_SUFFIX = 'augmented'

SELECTION_SUFFIX = 'selection'

BOUNDARY_SUFFIX = 'boundary'

X_LAYER = 'X'

gen_new_layer_key(key: str, sep: str = '_') → str

select_layer_data(layer: str, copy: bool = False, make_dense: bool = False) → numpy.ndarray | scipy.sparse.spmatrix

set_layer_data(layer: str, vals: numpy.ndarray, var_indices: numpy.ndarray | None = None, replace: bool = False)

get_adata_type() → str

adata_is_type(t: str) → bool

check_adata_is_type(argname: str = 'adata', optional: bool = False)

init_adata_type(t: str | None = None)

init_uns_pp_namespace()

init_uns_spatial_namespace()

set_uns_spatial_attribute(key: str, value: object)

get_uns_spatial_attribute(key: str) → object

has_uns_spatial_attribute(key: str) → bool

get_agg_bounds() → Tuple[int, int, int, int]

Get (xmin, xmax, ymin, ymax) for AGG type anndatas.

spateo.configuration.SKM

spateo.configuration.shiftedColorMap(cmap: matplotlib.colors.ListedColormap, start: float = 0, midpoint: float = 0.5, stop: float = 1.0, name: str = 'shiftedcmap') → matplotlib.colors.ListedColormap

Function to offset the “center” of a colormap. Useful for data with a negative min and positive max, and you want the middle of the colormap’s dynamic range to be at zero.

Parameters:

cmap

The matplotlib colormap to be altered

start

Offset from the lowest point in the colormap’s range. Defaults to 0.0 (no lower offset). Should be between 0.0 and midpoint.

midpoint

The new center of the colormap. Defaults to 0.5 (no shift). Should be between 0.0 and 1.0. In general, this should be 1 - vmax / (vmax + abs(vmin)) For example if your data range from -15.0 to +5.0, and you want the center of the colormap at 0.0, midpoint should be set to 1 - 5/(5 + 15)) or 0.75

stop

Offset from the highest point in the colormap’s range. Defaults to 1.0 (no upper offset). Should be between midpoint and 1.0.

name

the colormap name of the shifted colormap that will be registered.

Returns:

a new colormap that has the middle point of the colormap shifted.

Return type:

newcmap

spateo.configuration.fire_cmap

spateo.configuration.darkblue_cmap

spateo.configuration.darkgreen_cmap

spateo.configuration.darkred_cmap

spateo.configuration.darkpurple_cmap

spateo.configuration.div_blue_black_red_cmap

spateo.configuration.div_blue_red_cmap

spateo.configuration.glasbey_white_cmap

spateo.configuration.glasbey_dark_cmap

spateo.configuration._themes

spateo.configuration.reset_rcParams()

Reset matplotlib.rcParams to defaults.

spateo.configuration.zebrafish_colors = ['#4876ff', '#85C7F2', '#cd00cd', '#911eb4', '#000080', '#808080', '#008080', '#ffc125',...

spateo.configuration.cyc_10

spateo.configuration.cyc_20

spateo.configuration.zebrafish_256

spateo.configuration.spateo_theme(background='white')

spateo.configuration.config_spateo_rcParams(background: str = 'white', prop_cycle: List[str] = zebrafish_256, fontsize: int = 8, color_map: matplotlib.colors.ListedColormap = None, frameon: bool | None = None) → None

Configure matplotlib.rcParams to spateo defaults (based on ggplot style and scanpy).

Parameters:

background

The background color of the plot. By default, we use the white ground which is suitable for producing figures for publication. Setting it to black background will be great for presentation.

prop_cycle

A list with hex color codes

fontsize

Size of font

color_map

Color map

frameon

Whether to have frame for the figure.

Returns:

Nothing but configure the rcParams globally.

spateo.configuration.set_figure_params(spateo: bool = True, background: str = 'white', fontsize: int = 8, figsize: Tuple[int, int] = (6, 4), dpi: float | None = None, dpi_save: int | None = None, frameon: bool | None = None, vector_friendly: bool = True, color_map: str | None = None, format: str = 'pdf', transparent: bool = False, ipython_format: str = 'png2x') → None

Set resolution/size, styling and format of figures.

This function is adapted from: https://github.com/theislab/scanpy/blob/f539870d7484675876281eb1c475595bf4a69bdb/scanpy/_settings.py

Parameters:

spateo

bool (default: True) Init default values for matplotlib.rcParams suited for spateo.

background

str (default: white) The background color of the plot. By default we use the white ground which is suitable for producing figures for publication. Setting it to black background will be great for presentation.

fontsize

[float, float] or None (default: 6)

figsize

(float, float) (default: (6.5, 5)) Width and height for default figure size.

dpi

int or None (default: None) Resolution of rendered figures - this influences the size of figures in notebooks.

dpi_save

int or None (default: None) Resolution of saved figures. This should typically be higher to achieve publication quality.

frameon

bool or None (default: None) Add frames and axes labels to scatter plots.

vector_friendly

bool (default: True) Plot scatter plots using png backend even when exporting as pdf or svg.

color_map

str (default: None) Convenience method for setting the default color map.

format

{‘png’, ‘pdf’, ‘svg’, etc.} (default: ‘pdf’) This sets the default format for saving figures: file_format_figs.

transparent

bool (default: False) Save figures with transparent back ground. Sets rcParams[‘savefig.transparent’].

ipython_format

list of str (default: ‘png2x’) Only concerns the notebook/IPython environment; see IPython.core.display.set_matplotlib_formats for more details.

Returns:

Nothing but update the figure configurations.

spateo.configuration.set_pub_style(scaler: float = 1) → None

formatting helper function that can be used to save publishable figures

Parameters:

scaler

The multiplier to universally increase or decrease the font sizes.

Returns:

Nothing but set up the configuration for saving publishable figures.

spateo.configuration.set_pub_style_mpltex()

formatting helper function based on mpltex package that can be used to save publishable figures