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Sm.pl.voronoi

!!!

Short Description

sm.pl.voronoi: The function allows users to generate a voronoi diagram and color it based on any categorical column. Please note, voronoi diagrams are best fitted for small regions with upto 5000 cells. Any larger, the voronoi plots are uninterpretable and takes a long time to generate.

Function

voronoi(adata, color_by=None, colors=None, x_coordinate='X_centroid', y_coordinate='Y_centroid', imageid='imageid', subset=None, x_lim=None, y_lim=None, flip_y=True, voronoi_edge_color='black', voronoi_line_width=0.1, voronoi_alpha=0.5, size_max=np.inf, overlay_points=None, overlay_points_categories=None, overlay_drop_categories=None, overlay_points_colors=None, overlay_point_size=5, overlay_point_alpha=1, overlay_point_shape='.', plot_legend=True, legend_size=6, **kwargs)

Parameters:

Name Type Description Default
adata

Anndata object

required
color_by

string, optional
Color the voronoi diagram based on categorical variable (e.g. cell types or neighbourhoods). Pass the name of the column which contains the categorical variable.

None
colors

string or Dict, optional
Custom coloring the voronoi diagram. The parameter accepts sns color palettes or a python dictionary mapping the categorical variable with the required color.

None
x_coordinate

float, required
Column name containing the x-coordinates values.

'X_centroid'
y_coordinate

float, required
Column name containing the y-coordinates values.

'Y_centroid'
flip_y

bool, optional
Flip the Y-axis if needed. Some algorithms output the XY with the Y-coordinates flipped. If the image overlays do not align to the cells, try again by setting this to False.

True
imageid

string, optional
Column name of the column containing the image id.

'imageid'
subset

string, optional
imageid of a single image to be subsetted for plotting.

None
voronoi_edge_color

string, optional
A Matplotlib color for marking the edges of the voronoi. If facecolor is passed, the edge color will always be the same as the face color.

'black'
voronoi_line_width

float, optional
The linewidth of the marker edges. Note: The default edgecolors is 'face'. You may want to change this as well.

0.1
voronoi_alpha

float, optional
The alpha blending value, between 0 (transparent) and 1 (opaque).

0.5
x_lim

list, optional
Pass the x-coordinates range [x1,x2].

None
y_lim

list, optional
Pass the y-coordinates range [y1,y2].

None
overlay_points

string, optional
It is possible to overlay a scatter plot on top of the voronoi diagram. Pass the name of the column which contains categorical variable to be overlayed.

None
overlay_points_categories

list, optional
If the passed column in overlay_points contains multiple categories, however the user is only interested in a subset of categories, those specific names can be passed as a list. By default all categories will be overlayed on the voronoi diagram.

None
overlay_drop_categories

list, optional
Similar to overlay_points_categories. Here for ease of use, especially if large number of categories are present. The user can drop a set of categories.

None
overlay_points_colors

string or dict, optional
Similar to colors.
User can pass in a
a) solid color (like black)
b) sns palettes name (like Set1)
c) python dictionary mapping the categories with custom colors

None
overlay_point_size

float, optional
Overlay scatter plot point size.

5
overlay_point_alpha

float, optional
The alpha blending value for the overlay, between 0 (transparent) and 1 (opaque).

1
overlay_point_shape

string, optional
The marker style. marker can be either an instance of the class or the text shorthand for a particular marker.

'.'
plot_legend

bool, optional
Define if the figure legend should be plotted.
Please note the figure legend may be out of view and you may need to resize the image to see it, especially the legend for the scatter plot which will be on the left side of the plot.

True
legend_size

float, optional
Resize the legend if needed.

6
Example
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sm.pl.voronoi(adata, color_by='phenotype', colors=None, 
         x_coordinate='X_position', y_coordinate='Y_position',
         imageid='ImageId',subset=None,
         voronoi_edge_color = 'black',voronoi_line_width = 0.2, 
         voronoi_alpha = 0.5, size_max=np.inf,
         overlay_points='phenotype', overlay_points_categories=None, 
         overlay_drop_categories=None,
         overlay_point_size = 5, overlay_point_alpha= 1, 
         overlay_point_shape=".", plot_legend=False, legend_size=6)
Source code in scimap/plotting/_voronoi.py
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def voronoi (adata, color_by=None, colors=None, x_coordinate='X_centroid', y_coordinate='Y_centroid',
             imageid='imageid',subset=None, x_lim=None, y_lim=None, flip_y=True,
             voronoi_edge_color='black', voronoi_line_width=0.1, voronoi_alpha=0.5, size_max=np.inf,
             overlay_points=None, overlay_points_categories=None, overlay_drop_categories=None, overlay_points_colors=None,
             overlay_point_size = 5, overlay_point_alpha= 1, overlay_point_shape=".", plot_legend=True, legend_size = 6, **kwargs):
    """
Parameters:
    adata : Anndata object

    color_by : string, optional  
        Color the voronoi diagram based on categorical variable (e.g. cell types or neighbourhoods).
        Pass the name of the column which contains the categorical variable.

    colors : string or Dict, optional  
        Custom coloring the voronoi diagram. The parameter accepts `sns color palettes` or a python dictionary
        mapping the categorical variable with the required color.

    x_coordinate : float, required  
        Column name containing the x-coordinates values.

    y_coordinate : float, required  
        Column name containing the y-coordinates values.

    flip_y : bool, optional  
        Flip the Y-axis if needed. Some algorithms output the XY with the Y-coordinates flipped.
        If the image overlays do not align to the cells, try again by setting this to `False`.

    imageid : string, optional  
        Column name of the column containing the image id.

    subset : string, optional  
        imageid of a single image to be subsetted for plotting.

    voronoi_edge_color : string, optional  
        A Matplotlib color for marking the edges of the voronoi. 
        If `facecolor` is passed, the edge color will always be the same as the face color.

    voronoi_line_width : float, optional  
        The linewidth of the marker edges. Note: The default edgecolors is 'face'. You may want to change this as well. 

    voronoi_alpha : float, optional  
        The alpha blending value, between 0 (transparent) and 1 (opaque).

    x_lim : list, optional  
        Pass the x-coordinates range [x1,x2].

    y_lim : list, optional  
        Pass the y-coordinates range [y1,y2].

    overlay_points : string, optional  
        It is possible to overlay a scatter plot on top of the voronoi diagram.
        Pass the name of the column which contains categorical variable to be overlayed.

    overlay_points_categories : list, optional  
        If the passed column in `overlay_points` contains multiple categories, however the user is only
        interested in a subset of categories, those specific names can be passed as a list. By default all 
        categories will be overlayed on the voronoi diagram.

    overlay_drop_categories : list, optional  
        Similar to `overlay_points_categories`. Here for ease of use, especially if large number of categories are present.
        The user can drop a set of categories.

    overlay_points_colors : string or dict, optional  
        Similar to `colors`.  
        User can pass in a  
        a) solid color (like `black`)  
        b) sns palettes name (like `Set1`)  
        c) python dictionary mapping the categories with custom colors

    overlay_point_size : float, optional  
        Overlay scatter plot point size.

    overlay_point_alpha : float, optional  
        The alpha blending value for the overlay, between 0 (transparent) and 1 (opaque).

    overlay_point_shape : string, optional  
        The marker style. marker can be either an instance of the class or the text shorthand for a particular marker.

    plot_legend : bool, optional  
        Define if the figure legend should be plotted.  
        Please note the figure legend may be out of view and you may need to resize the image to see it, especially 
        the legend for the scatter plot which will be on the left side of the plot.

    legend_size : float, optional  
        Resize the legend if needed.

Example:

    ```python
    sm.pl.voronoi(adata, color_by='phenotype', colors=None, 
             x_coordinate='X_position', y_coordinate='Y_position',
             imageid='ImageId',subset=None,
             voronoi_edge_color = 'black',voronoi_line_width = 0.2, 
             voronoi_alpha = 0.5, size_max=np.inf,
             overlay_points='phenotype', overlay_points_categories=None, 
             overlay_drop_categories=None,
             overlay_point_size = 5, overlay_point_alpha= 1, 
             overlay_point_shape=".", plot_legend=False, legend_size=6)

    ```

    """


    # create the data frame needed
    data = adata.obs

    # Subset the image of interest
    if subset is not None:
        data = data[data[imageid] == subset]


    # subset coordinates if needed
    if x_lim is not None:
        x1 = x_lim [0]
        if len(x_lim) < 2:
            x2 = max(data[x_coordinate])
        else:
            x2 = x_lim [1]
    if y_lim is not None:
        y1 = y_lim [0]
        if len(y_lim) < 2:
            y2 = min(data[y_coordinate])
        else:
            y2 = y_lim [1]
    # do the actuall subsetting
    if x_lim is not None:
        data = data[data[x_coordinate] >= x1]
        data = data[data[x_coordinate] <= x2]
    if y_lim is not None:
        data = data[data[y_coordinate] <= y1]
        data = data[data[y_coordinate] >= y2]


    # create an extra column with index information
    data['index_info'] = np.arange(data.shape[0])

    # generate the x and y coordinates
    points = data[[x_coordinate,y_coordinate]].values

    # invert the Y-axis
    if flip_y is True:
        points[:,1] = max(points[:,1])-points[:,1]

    # Generate colors
    if color_by is None:
        colors = np.repeat('#e5e5e5', len(data))
#    elif color_by is None and colors is not None:
#        if isinstance(colors,str):
#            colors = np.repeat(colors, len(data))
    elif color_by is not None and colors is None:
        # auto color the samples
        if len(np.unique(data[color_by])) <= 9:
            c = sns.color_palette('Set1')[0:len(np.unique(data[color_by]))]
        if len(np.unique(data[color_by])) > 9 and len(np.unique(data[color_by])) <= 20:
            c = sns.color_palette('tab20')[0:len(np.unique(data[color_by]))]
        if len(np.unique(data[color_by])) > 20:
            # For large categories generate random colors 
            np.random.seed(0) ; c = np.random.rand(len(np.unique(data[color_by])),3).tolist()
        # merge colors with phenotypes/ categories of interest
        p = np.unique(data[color_by])
        c_p = dict(zip(p, c))
        # map to colors
        colors = list(map(c_p.get, list(data[color_by].values)))
    elif color_by is not None and colors is not None:
        # check if colors is a dictionary or a sns color scale
        if isinstance(colors,str): 
            if len(sns.color_palette(colors)) < len(np.unique(data[color_by])):
                raise ValueError(str(colors) + ' includes a maximun of ' + str(len(sns.color_palette(colors))) + ' colors, while your data need '  + str(len(np.unique(data[color_by]))) + ' colors')
            else:
                c = sns.color_palette(colors)[0:len(np.unique(data[color_by]))]    
                # merge colors with phenotypes/ categories of interest
                p = np.unique(data[color_by])
                c_p = dict(zip(p, c))
        if isinstance(colors,dict):
            if len(colors) < len(np.unique(data[color_by])):
                raise ValueError('Color mapping is not provided for all categories. Please check')
            else:
                c_p = colors
        # map to colors
        colors = list(map(c_p.get, list(data[color_by].values)))



    # create the voronoi object
    vor = Voronoi(points)

    # trim the object
    regions, vertices = voronoi_finite_polygons_2d(vor)

    # plotting
    pts = MultiPoint([Point(i) for i in points])
    mask = pts.convex_hull
    new_vertices = []
    if type(voronoi_alpha)!=list:
        voronoi_alpha = [voronoi_alpha]*len(points)
    areas = []
    for i,(region,alph) in enumerate(zip(regions,voronoi_alpha)):
        polygon = vertices[region]
        shape = list(polygon.shape)
        shape[0] += 1
        p = Polygon(np.append(polygon, polygon[0]).reshape(*shape)).intersection(mask)
        areas+=[p.area]
        if p.area <size_max:
            poly = np.array(list(zip(p.boundary.coords.xy[0][:-1], p.boundary.coords.xy[1][:-1])))
            new_vertices.append(poly)
            if voronoi_edge_color == 'facecolor':
                plt.fill(*zip(*poly), alpha=alph, edgecolor=colors[i], linewidth = voronoi_line_width , facecolor = colors[i])
                plt.xticks([]) ; plt.yticks([]);
            else:
                plt.fill(*zip(*poly), alpha=alph, edgecolor=voronoi_edge_color, linewidth = voronoi_line_width, facecolor = colors[i])
                plt.xticks([]) ; plt.yticks([]);
                #plt.xlim([1097.5,1414.5])
                #plt.ylim([167.3,464.1])


    # Add scatter on top of the voronoi if user requests
    if overlay_points is not None:
        if overlay_points_categories is None:
            d = data
        if overlay_points_categories is not None:
            # convert to list if needed (cells to keep)
            if isinstance(overlay_points_categories,str): 
                overlay_points_categories = [overlay_points_categories]
            # subset cells needed
            d = data[data[overlay_points].isin(overlay_points_categories)]    
        if overlay_drop_categories is not None:
            # conver to list if needed (cells to drop)
            if isinstance(overlay_drop_categories,str): 
                overlay_drop_categories = [overlay_drop_categories]
            # subset cells needed
            d = d[-d[overlay_points].isin(overlay_drop_categories)]

        # Find the x and y coordinates for the overlay category
        #points_scatter = d[[x_coordinate,y_coordinate]].values
        points_scatter = points[d.index_info.values]

        # invert the Y-axis
        #points_scatter[:,1] = max(points_scatter[:,1])-points_scatter[:,1]

        # Generate colors for the scatter plot
        if overlay_points_colors is None and color_by == overlay_points:
            # Borrow color from vornoi
            wanted_keys = np.unique(d[overlay_points]) # The keys to extract
            c_p_scatter = dict((k, c_p[k]) for k in wanted_keys if k in c_p)
        elif overlay_points_colors is None and color_by != overlay_points:
            # Randomly generate colors for all the categories in scatter plot
            # auto color the samples
            if len(np.unique(d[overlay_points])) <= 9:
                c_scatter = sns.color_palette('Set1')[0:len(np.unique(d[overlay_points]))]
            if len(np.unique(d[overlay_points])) > 9 and len(np.unique(d[overlay_points])) <= 20:
                c_scatter = sns.color_palette('tab20')[0:len(np.unique(d[overlay_points]))]
            if len(np.unique(d[overlay_points])) > 20:
                # For large categories generate random colors 
                np.random.seed(1) ; c_scatter = np.random.rand(len(np.unique(d[overlay_points])),3).tolist()
            # merge colors with phenotypes/ categories of interest
            p_scatter = np.unique(d[overlay_points])
            c_p_scatter = dict(zip(p_scatter, c_scatter))
        elif  overlay_points_colors is not None:
            # check if the overlay_points_colors is a pallete
            if isinstance(overlay_points_colors,str):
                try:
                    c_scatter = sns.color_palette(overlay_points_colors)[0:len(np.unique(d[overlay_points]))]
                    if len(sns.color_palette(overlay_points_colors)) < len(np.unique(d[overlay_points])):
                        raise ValueError(str(overlay_points_colors) + ' pallete includes a maximun of ' + str(len(sns.color_palette(overlay_points_colors))) + ' colors, while your data (overlay_points_colors) need '  + str(len(np.unique(d[overlay_points]))) + ' colors') 
                except:
                    c_scatter = np.repeat(overlay_points_colors,len(np.unique(d[overlay_points])))   #[overlay_points_colors]
                # create a dict
                p_scatter = np.unique(d[overlay_points])
                c_p_scatter = dict(zip(p_scatter, c_scatter))
            if isinstance(overlay_points_colors,dict):
                if len(overlay_points_colors) < len(np.unique(d[overlay_points])):
                    raise ValueError('Color mapping is not provided for all categories. Please check overlay_points_colors')
                else:
                    c_p_scatter = overlay_points_colors
        # map to colors
        colors_scatter = list(map(c_p_scatter.get, list(d[overlay_points].values)))

        #plt.scatter(x = points_scatter[:,0], y = points_scatter[:,1], s= overlay_point_size, alpha= overlay_point_alpha, c= colors_scatter, marker=overlay_point_shape)
        plt.scatter(x = points_scatter[:,0], y = points_scatter[:,1], s= overlay_point_size, alpha= overlay_point_alpha, c= colors_scatter, marker=overlay_point_shape,**kwargs)
        plt.xticks([]) ; plt.yticks([]);


    if plot_legend is True:
        # Add legend to voronoi
        patchList = []
        for key in c_p:
                data_key = mpatches.Patch(color=c_p[key], label=key)
                patchList.append(data_key)

        first_legend = plt.legend(handles=patchList, bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0., prop={'size': legend_size})
        plt.tight_layout()
        # Add the legend manually to the current Axes.
        ax = plt.gca().add_artist(first_legend)

        if overlay_points is not None:
            # Add legend to scatter
            patchList_scatter = []
            for key in c_p_scatter:
                    data_key_scatter = mpatches.Patch(color=c_p_scatter[key], label=key)
                    patchList_scatter.append(data_key_scatter)

            plt.legend(handles=patchList_scatter, bbox_to_anchor=(-0.05, 1), loc=1, borderaxespad=0., prop={'size': legend_size})