spateo.plotting.static.geo ========================== .. py:module:: spateo.plotting.static.geo .. autoapi-nested-parse:: Plotting functions for spatial geometry plots. Functions --------- .. autoapisummary:: spateo.plotting.static.geo.geo spateo.plotting.static.geo.space_polygons spateo.plotting.static.geo.create_polygon_object_nanostring Module Contents --------------- .. py:function:: geo(adata: anndata.AnnData, basis: str = 'contour', color: Union[list, str, None] = None, genes: Union[list, None] = [], gene_cmaps: Optional[str] = None, dpi: int = 100, alpha: float = 0.8, boundary_width: float = 0.2, boundary_color='black', stack_genes: bool = False, stack_genes_threshold: float = 0.01, stack_colors_legend_size: int = 10, figsize: Tuple[float, float] = (6, 6), aspect: str = 'equal', slices: Optional[int] = None, img_layers: Optional[int] = None, *args, **kwargs) Geometry plot for physical coordinates of each cell. :param adata: an Annodata object that contain the physical coordinates for each bin/cell, etc. :param basis: The key to the column in adata.obs from which the contour of the cell segmentation will be generated. :param color: Any or any list of column names or gene name, etc. that will be used for coloring cells. If `color` is not None, stack_genes will be disabled automatically because `color` can contain non numerical values. :param genes: The gene list that will be used to plot the gene expression on the same scatter plot. Each gene will have a different color. Can be a single gene name string and we will convert it to a list. :param gene_cmaps: The colormap used to stack different genes in a single plot. :param dpi: 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 height. 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 :param alpha: The alpha value of the cells. :param boundary_width: The line width of boundary. :param boundary_color: The color value of boundary. :param stack_genes: whether to show all gene plots on the same plot :param stack_genes_threshold: lower bound of gene values that will be drawn on the plot. :param stack_colors_legend_size: control the size of legend when stacking genes :param figuresize: size of the figure. :param 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 :param slices: The index to the tissue slice, will used in adata.uns["spatial"][slices]. :param img_layers: The index to the (staining) image of a tissue slice, will be used in adata.uns["spatial"][slices]["images"]. :rtype: plots gene or cell feature of the adata object on the physical spatial coordinates. .. py:function:: space_polygons(polygons_path: str, adata: anndata.AnnData, color: Optional[Union[List[str], str]] = None, fov: Optional[Union[int, str]] = None, **kwargs) Plot polygons on spatial coordinates. :param polygons_path: The path to the file containing polygon coordinates :param adata: The AnnData object that contains the spatial coordinates, gene expression, cell type labels, etc. :param color: The column name in the adata.obs that will be used to color the polygons. :param fov: The fov name that will be used to select the polygons. If None, all polygons will be plotted. :param kwargs: Additional arguments passed to :func ~`spateo.pl.geo.geo()`. .. py:function:: create_polygon_object_nanostring(polygon_df: pandas.DataFrame) Process cell data to construct contours and calculate area and centroid. :param polygon_df: Input DataFrame containing pixel-to-cell correspondence data with columns 'cellID_fov', 'x_local_px', and 'y_local_px'. :returns: Dataframe containing polygon information. Contains columns 'label', 'area', 'bbox-0', 'bbox-1', 'bbox-2', 'bbox-3', 'centroid-0', 'centroid-1', and 'contour'. Indexed by the 'label' column. :rtype: processed_polygon_df