pl

heatmap(adata, topic_prop, groupby, dendrogram=False, swap_axes=True, cmap=None, figsize=(10, 5), save=None, **kwargs)

Creates a heatmap of cell(grouped by groupby) by topics

Parameters:

Name	Type	Description	Default
adata	_type_	Adata object	required
topic_prop	_type_	Topic proportions returned by STAMP	required
groupby	_type_	Column in adata object to arrange the cells	required
figsize	tuple	Figsize. Defaults to (10, 5).	(10, 5)
dendrogram	bool	Whether to cluster. Defaults to False.	False
swap_axes	bool	Whether to swap x and y axis. Defaults to True.	True
cmap	_type_	What matplotib cmap to use. Defaults to None.	None
save	_type_	Whether to save the object. Defaults to None.	None

matrixplot(adata, topic_prop, groupby, dendrogram=False, swap_axes=True, cmap=None, figsize=(10, 5), save=None, **kwargs)

Creates a matrixplot of cell(grouped by groupby) by topics

Parameters:

Name	Type	Description	Default
adata	_type_	Adata object	required
topic_prop	_type_	Topic proportions returned by STAMP	required
groupby	_type_	Column in adata object to arrange the cells	required
figsize	tuple	Figsize. Defaults to (10, 5).	(10, 5)
dendrogram	bool	Whether to cluster. Defaults to False.	False
swap_axes	bool	Whether to swap x and y axis. Defaults to True.	True
cmap	_type_	What matplotib cmap to use. Defaults to None.	None
save	_type_	Whether to save the object. Defaults to None.	None

trackplot(adata, topic_prop, groupby, dendrogram=False, swap_axes=True, cmap=None, figsize=(10, 5), save=None, **kwargs)

Creates a trackplot of cell(grouped by groupby) by topics

Parameters:

Name	Type	Description	Default
adata	_type_	Adata object	required
topic_prop	_type_	Topic proportions returned by STAMP	required
groupby	_type_	Column in adata object to arrange the cells	required
figsize	tuple	Figsize. Defaults to (10, 5).	(10, 5)
dendrogram	bool	Whether to cluster. Defaults to False.	False
swap_axes	bool	Whether to swap x and y axis. Defaults to True.	True
cmap	_type_	What matplotib cmap to use. Defaults to None.	None
save	_type_	Whether to save the object. Defaults to None.	None

spatialpie(adata, color, N=2, *, basis='spatial', img=None, img_key=_empty, library_id=_empty, crop_coord=None, alpha_img=1.0, bw=False, frameon=False, size=1.0, scale_factor=None, spot_size=None, na_color=None, show=None, return_fig=None, cmap='tab20', legend=True, figsize=None, title=None)

Creates a spatialpie plot of object. Very ugly according to twitter.

Parameters:

Name	Type	Description	Default
adata	_type_	Adata object	required
topic_prop	_type_	Return	required
basis	str	Basis to use. Defaults to "spatial".	'spatial'
img	Union[np.ndarray, None]	description. Defaults to None.	None
img_key	Union[str, None, Empty]	description. Defaults to _empty.	_empty
library_id	Union[str, Empty]	description. Defaults to _empty.	_empty
crop_coord	Tuple[int, int, int, int]	description.	None
alpha_img	float	description. Defaults to 1.0.	1.0
bw	Optional[bool]	description. Defaults to False.	False
frameon	bool	description. Defaults to False.	False
size	float	description. Defaults to 1.0.	1.0
scale_factor	Optional[float]	description. Defaults to None.	None
spot_size	Optional[float]	description. Defaults to None.	None
na_color	Optional[ColorLike]	description. Defaults to None.	None
show	Optional[bool]	description. Defaults to None.	None
return_fig	Optional[bool]	description. Defaults to None.	None
cmap	str	description. Defaults to "tab20".	'tab20'
legend	bool	description. Defaults to True.	True
figsize	_type_	description. Defaults to None.	None
title	_type_	description. Defaults to None.	None

Returns:

Type	Description
Union[Axes, List[Axes], None]	Union[Axes, List[Axes], None]: description

get_rgb_function(cmap, min_value, max_value)

Generate a function to map continous values to RGB values using colormap between min_value & max_value.

rgb_to_ryb(rgb)

Converts colours from RGB colorspace to RYB

Parameters

rgb numpy array Nx3

Returns

Numpy array Nx3

ryb_to_rgb(ryb)

Converts colours from RYB colorspace to RGB

Parameters

ryb numpy array Nx3

Returns

Numpy array Nx3

plot_spatial(adata, topic_prop, basis='spatial', bw=False, img=None, library_id=_empty, crop_coord=None, img_key=_empty, spot_size=None, na_color=None, scale_factor=None, scale_default=0.5, show_img=True, display_zeros=False, figsize=(10, 10), **kwargs)

Plot taken from cell2location at https://github.com/BayraktarLab/cell2location. Able to display zeros and also on umap through the basis function

Parameters:

Name	Type	Description	Default
adata	_type_	Adata object with spatial coordinates in adata.obsm['spatial']	required
topic_prop	_type_	Topic proportion obtained from STAMP.	required
basis	str	Which basis to plot in adata.obsm. Defaults to "spatial".	'spatial'
bw	bool	Defaults to False.	False
img	_type_	. Defaults to None.	None
library_id	_type_	description. Defaults to _empty.	_empty
crop_coord	_type_	description. Defaults to None.	None
img_key	_type_	description. Defaults to _empty.	_empty
spot_size	_type_	description. Defaults to None.	None
na_color	_type_	description. Defaults to None.	None
scale_factor	_type_	description. Defaults to None.	None
scale_default	float	description. Defaults to 0.5.	0.5
show_img	bool	Whether to display spatial image. Sets to false	True
display_zeros	bool	Whether to display cells that have low counts	False
figsize	tuple	Figsize of image. Defaults to (10, 10).	(10, 10)

Returns:

Name	Type	Description
_type_		Function taken from cell2location at
https		//cell2location.readthedocs.io/en/latest/_modules/cell2location/plt/plot_spatial.html#plot_spatial.
		Able to plot both on spatial and umap coordinates. Still very raw.

spatial(adata, color=None, cmap=None, frameon=None, title=None, wspace=None, hspace=0.25, palette=None, colorbar_loc='right', size=1, basis='spatial', vmax=None, ncols=4, layer=None, show=True, *args, **kwargs)

A faster simple function that uses sc.pl.embedding to plot for non-visium data so it dont take too long. ~sleep. Very inflexible.

Parameters:

Name	Type	Description	Default
adata	_type_	Annotated data matrix.	required
color	_type_	Keys for annotations of observations/cells or variables/genes	None
size	int	size of spots. Defaults to 1.	1
basis	str	basis in obsm. Defaults to "spatial".	'spatial'
vmax	str	The value representing the upper limit of the color scale. Defaults to "p99".	None
show	bool	Show the plot, do not return axis. Defaults to True.	True

Returns:

Name	Type	Description
_type_		A plot