spateo.plotting.static.scatters

Module Contents

Functions

scatters([show_legend])

Plot an embedding as points. Currently, this only works

spateo.plotting.static.scatters.scatters(adata: anndata.AnnData, basis: Union[str, list] = 'umap', vf_key: Optional[str] = None, X_grid: Optional[numpy.ndarray] = None, V: Optional[numpy.ndarray] = None, x: int = 0, y: int = 1, z: int = 2, color: Union[str, list] = 'ntr', layer: Union[str, list] = 'X', highlights: Optional[list] = None, labels: Optional[list] = None, values: Optional[list] = None, theme: Optional[str] = None, cmap: Optional[str] = None, color_key: Union[dict, list] = None, color_key_cmap: Optional[str] = None, background: Optional[str] = None, ncols: int = 4, pointsize: Union[None, float] = None, figsize: tuple = (6, 4), show_legend='on data', use_smoothed: bool = True, aggregate: Optional[str] = None, show_arrowed_spines: bool = False, ax: Optional[matplotlib.axes.Axes] = None, sort: str = 'raw', save_show_or_return: typing_extensions.Literal[save, show, return, both, all] = 'show', save_kwargs: Optional[Dict] = None, return_all: bool = False, add_gamma_fit: bool = False, frontier: bool = False, contour: bool = False, ccmap: Optional[str] = None, alpha: float = 0.1, calpha: float = 0.4, sym_c: bool = False, smooth: bool = False, dpi: int = 100, inset_dict: dict = {}, marker: str = None, group: str = None, add_group_gamma_fit: bool = False, affine_transform_degree: int = None, affine_transform_A: Optional[numpy.ndarray] = None, affine_transform_b: Optional[numpy.ndarray] = None, stack_colors: bool = False, stack_colors_threshold: float = 0.001, stack_colors_title: str = 'stacked colors', stack_colors_legend_size: int = 2, stack_colors_cmaps: Optional[str] = None, despline: bool = True, deaxis: bool = True, despline_sides: Union[None, List[str]] = None, projection: str = '2d', geo: bool = False, boundary_width: float = 0.2, boundary_color: str = 'black', aspect: str = 'auto', slices: Optional[int] = None, img_layers: Optional[int] = None, vf_plot_method: typing_extensions.Literal[cell, grid, stream] = 'cell', vf_kwargs: Optional[Dict[str, Union[str, int, float]]] = None, **kwargs) → None | matplotlib.axes.Axes

Plot an embedding as points. Currently, this only works for 2D embeddings. While there are many optional parameters to further control and tailor the plotting, you need only pass in the trained/fit umap model to get results. This plot utility will attempt to do the hard work of avoiding overplotting issues, and make it easy to automatically colour points by a categorical labelling or numeric values. This method is intended to be used within a Jupyter notebook with %matplotlib inline.

Parameters:

adata

AnnData an Anndata object

basis

str The reduced dimension.

vf_key

Optional, key in .obsm containing vector field information

X_grid

Optional, array containing grid points for vector field plots

V

Optional, array containing vector fields

x

int (default: 0) The column index of the low dimensional embedding for the x-axis.

y

int (default: 1) The column index of the low dimensional embedding for the y-axis.

color

string (default: ntr) Any column names or gene expression, etc. that will be used for coloring cells.

layer

str (default: X) The layer of data to use for the scatter plot.

highlights

list (default: None) Which color group will be highlighted. if highlights is a list of lists - each list is relate to each color element.

labels

array, shape (n_samples,) (optional, default None) An array of labels (assumed integer or categorical), one for each data sample. This will be used for coloring the points in the plot according to their label. Note that this option is mutually exclusive to the values option.

values

array, shape (n_samples,) (optional, default None) An array of values (assumed float or continuous), one for each sample. This will be used for coloring the points in the plot according to a colorscale associated to the total range of values. Note that this option is mutually exclusive to the labels option.

theme

string (optional, default None) A color theme to use for plotting. A small set of predefined themes are provided which have relatively good aesthetics. Available themes are:

• ’blue’

• ’red’

• ’green’

• ’inferno’

• ’fire’

• ’viridis’

• ’darkblue’

• ’darkred’

• ’darkgreen’

cmap

string (optional, default ‘Blues’) The name of a matplotlib colormap to use for coloring or shading points. If no labels or values are passed this will be used for shading points according to density (largely only of relevance for very large datasets). If values are passed this will be used for shading according the value. Note that if theme is passed then this value will be overridden by the corresponding option of the theme.

color_key

dict or array, shape (n_categories) (optional, default None) A way to assign colors to categoricals. This can either be an explicit dict mapping labels to colors (as strings of form ‘#RRGGBB’), or an array like object providing one color for each distinct category being provided in labels. Either way this mapping will be used to color points according to the label. Note that if theme is passed then this value will be overridden by the corresponding option of the theme.

color_key_cmap

The name of a matplotlib colormap to use for categorical coloring. If an explicit color_key is not given a color mapping for categories can be generated from the label list and selecting a matching list of colors from the given colormap. Note that if theme is passed then this value will be overridden by the corresponding option of the theme.

background

string or None (optional, default ‘None`) The color of the background. Usually this will be either ‘white’ or ‘black’, but any color name will work. Ideally one wants to match this appropriately to the colors being used for points etc. This is one of the things that themes handle for you. Note that if theme is passed then this value will be overridden by the corresponding option of the theme.

ncols

int (optional, default 4) Number of columns for the figure.

pointsize

None or float (default: None) The scale of the point size. Actual point cell size is calculated as 500.0 / np.sqrt(adata.shape[0]) * pointsize

figsize

None or [float, float] (default: None) The width and height of a figure.

show_legend

bool (optional, default True) Whether to display a legend of the labels

use_smoothed

bool (optional, default True) Whether to use smoothed values (i.e. M_s / M_u instead of spliced / unspliced, etc.).

aggregate

str or None (default: None) The column in adata.obs that will be used to aggregate data points.

show_arrowed_spines

bool (optional, default False) Whether to show a pair of arrowed spines representing the basis of the scatter is currently using.

ax

matplotlib.Axis (optional, default None) The matplotlib axes object where new plots will be added to. Only applicable to drawing a single component.

sort

str (optional, default raw) The method to reorder data so that high values points will be on top of background points. Can be one of {‘raw’, ‘abs’, ‘neg’}, i.e. sorted by raw data, sort by absolute values or sort by negative values.

save_show_or_return

Whether to save, show or return the figure. If “both”, it will save and plot the figure at the same time. If “all”, the figure will be saved, displayed and the associated axis and other object will be return.

save_kwargs

A dictionary that will be passed to the save_fig function. By default, it is an empty dictionary and the save_fig function will use the {“path”: None, “prefix”: ‘scatter’, “dpi”: None, “ext”: ‘pdf’, “transparent”: True, “close”: True, “verbose”: True} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs.

return_all

bool (default: False) Whether to return all the scatter related variables. Default is False.

add_gamma_fit

bool (default: False) Whether to add the line of the gamma fitting. This will automatically turn on if basis points to gene names and those genes have went through gamma fitting.

frontier

bool (default: False) Whether to add the frontier. Scatter plots can be enhanced by using transparency (alpha) in order to show area of high density and multiple scatter plots can be used to delineate a frontier. See matplotlib tips & tricks cheatsheet (https://github.com/matplotlib/cheatsheets). Originally inspired by figures from scEU-seq paper: https://science.sciencemag.org/content/367/6482/1151. If contour is set to be True, frontier will be ignored as contour also add an outlier for data points.

contour

bool (default: False) Whether to add an countor on top of scatter plots. We use tricontourf to plot contour for non-gridded data. The shapely package was used to create a polygon of the concave hull of the scatters. With the polygon we then check if the mean of the triangulated points are within the polygon and use this as our condition to form the mask to create the contour. We also add the polygon shape as a frontier of the data point (similar to when setting frontier = True). When the color of the data points is continuous, we will use the same cmap as for the scatter points by default, when color is categorical, no contour will be drawn but just the polygon. cmap can be set with ccmap argument. See below. This has recently changed to use seaborn’s kdeplot.

ccmap

str or None (default: None) The name of a matplotlib colormap to use for coloring or shading points the contour. See above.

calpha

float (default: 0.4) Contour alpha value passed into sns.kdeplot. The value should be inbetween [0, 1]

sym_c

bool (default: False) Whether do you want to make the limits of continuous color to be symmetric, normally this should be used for plotting velocity, jacobian, curl, divergence or other types of data with both positive or negative values.

smooth

bool or int (default: False) Whether do you want to further smooth data and how much smoothing do you want. If it is False, no smoothing will be applied. If True, smoothing based on one step diffusion of connectivity matrix (.uns[‘moment_cnn’] will be applied. If a number larger than 1, smoothing will based on `smooth steps of diffusion.

dpi

float, (default: 100.0) The resolution of the figure in dots-per-inch. Dots per inches (dpi) determines how many pixels the figure comprises. dpi is different from ppi or points per inches. Note that most elements like lines, markers, texts have a size given in points so you can convert the points to inches. Matplotlib figures use Points per inch (ppi) of 72. A line with thickness 1 point will be 1./72. inch wide. A text with fontsize 12 points will be 12./72. inch heigh. Of course if you change the figure size in inches, points will not change, so a larger figure in inches still has the same size of the elements.Changing the figure size is thus like taking a piece of paper of a different size. Doing so, would of course not change the width of the line drawn with the same pen. On the other hand, changing the dpi scales those elements. At 72 dpi, a line of 1 point size is one pixel strong. At 144 dpi, this line is 2 pixels strong. A larger dpi will therefore act like a magnifying glass. All elements are scaled by the magnifying power of the lens. see more details at answer 2 by @ImportanceOfBeingErnest: https://stackoverflow.com/questions/47633546/relationship-between-dpi-and-figure-size

inset_dict

dict (default: {}) A dictionary of parameters in inset_ax. Example, something like {“width”: “5%”, “height”: “50%”, “loc”: ‘lower left’, “bbox_to_anchor”: (0.85, 0.90, 0.145, 0.145), “bbox_transform”: ax.transAxes, “borderpad”: 0} See more details at https://matplotlib.org/api/_as_gen/mpl_toolkits.axes_grid1.inset_locator.inset_axes.html or https://stackoverflow.com/questions/39803385/what-does-a-4-element-tuple-argument-for-bbox-to-anchor-mean -in-matplotlib

marker

str (default: None) The marker style. marker can be either an instance of the class or the text shorthand for a particular marker. See matplotlib.markers for more information about marker styles.

group

The key to the column in adata.obs that points to cell groups that will be used to include the gamma fittings.

add_group_gamma_fit

Whether or not to add the gamma fitting line for each cell group.

affine_transform_degree

Transform coordinates of points according to some degree.

affine_transform_A

Coefficients in affine transformation Ax + b. 2D for now.

affine_transform_b

Bias in affine transformation Ax + b.

stack_colors

Whether to stack all color on the same ax passed above. Currently only support 18 sequential matplotlib default cmaps assigning to different color groups. (#colors should be smaller than 18, reuse if #colors > 18. To-do: generate cmaps according to #colors)

stack_colors_threshold

A threshold for filtering points values < threshold when drawing each color. E.g. if you do not want points with values < 1 showing up on axis, set threshold to be 1

stack_colors_title

The title for the stack_color plot.

stack_colors_legend_size

Control the legend size in stack color plot.

stack_colors_cmaps

The colormap used to stack different genes in a single plot.

despline

Whether to remove splines of the figure.

despline_sides

Which side of splines should be removed. Can be any combination of [“bottom”, “right”, “top”, “left”].

deaxis

Whether to remove axis ticks of the figure.

projection

The projection of the figure. Can be “2d”, “3d”, “polar”, etc.

geo

bool (default: False) Use geometry info or not.

boundary_width

float, (default: 0.2) The line width of boundary.

boundary_color

(default: “black”) The color value of boundary.

aspect

Set the aspect of the axis scaling, i.e. the ratio of y-unit to x-unit. In physical spatial plot, the default is ‘equal’. See more details at: https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.set_aspect.html

slices

The index to the tissue slice, will used in adata.uns[“spatial”][slices].

img_layers

The index to the (staining) image of a tissue slice, will be used in adata.uns[“spatial”][slices][“images”].

vf_plot_method

The method used to plot the vector field. Can be one of the following: ‘cell’: Plot the vector field at the center of each cell. ‘grid’: Plot the vector field on a grid. ‘stream’: Plot the vector field as stream lines.

vf_kwargs

Optional dictionary containing parameters for vector field plotting

kwargs

Additional arguments passed to plt functions (plt.scatters, plt.quiver, plt.streamplot).

Returns:

Either None or a matplotlib axis with the relevant plot displayed. If you are using a notbooks and have %matplotlib inline set then this will simply display inline.

Return type:

result