spatial_scatterPlot

Short Description

The scatterPlot function offers a convenient way to generate scatter plots for visualizing single-cell spatial data. By utilizing this function, users can effectively visualize the spatial distribution of cells while overlaying expression levels or categorical columns onto the plot. This functionality allows for a comprehensive understanding of the relationship between cell location and specific features of interest within the dataset.

Function

spatial_scatterPlot(adata, colorBy, topLayer=None, x_coordinate='X_centroid', y_coordinate='Y_centroid', imageid='imageid', layer=None, subset=None, s=None, ncols=None, alpha=1, dpi=200, fontsize=None, plotLegend=True, cmap='RdBu_r', catCmap='tab20', vmin=None, vmax=None, customColors=None, figsize=(5, 5), invert_yaxis=True, saveDir=None, fileName='scimapScatterPlot.png', **kwargs)

Parameters:

Name	Type	Description	Default
adata	AnnData	Pass the adata loaded into memory or a path to the adata file (.h5ad).	required
colorBy	str		required
topLayer	list	A list of categories that should be plotted on the top layer. These categories must be present in the `colorBy` data. Helps to highlight cell types or cluster that is of interest.	None
x_coordinate	str	The column name in spatial feature table that records the X coordinates for each cell.	'X_centroid'
y_coordinate	str	The column name in single-cell spatial table that records the Y coordinates for each cell.	'Y_centroid'
imageid	str	The column name in spatial feature table that contains the image ID for each cell.	'imageid'
layer	str or None	The layer in adata.layers that contains the expression data to use. If None, adata.X is used. use raw to use the data stored in adata.raw.X.	None
subset	list or None	imageid of a single or multiple images to be subsetted for plotting purposes.	None
s	float	The size of the markers.	None
ncols	int	The number of columns in the final plot when multiple variables are plotted.	None
alpha	float	The alpha value of the points (controls opacity).	1
dpi	int	The DPI of the figure.	200
fontsize	int	The size of the fonts in plot.	None
plotLegend	bool	Whether to include a legend.	True
cmap	str	The colormap to use for continuous data.	'RdBu_r'
catCmap	str	The colormap to use for categorical data.	'tab20'
vmin	float or None	The minimum value of the color scale.	None
vmax	float or None	The maximum value of the color scale.	None
customColors	dict or None	A dictionary mapping color categories to colors.	None
figsize	tuple	The size of the figure. Default is (5, 5).	(5, 5)
invert_yaxis	bool	Invert the Y-axis of the plot.	True
saveDir	str or None	The directory to save the output plot. If None, the plot will not be saved.	None
fileName	str	The name of the output file. Use desired file format as suffix (e.g. .png or .pdf). Default is 'scimapScatterPlot.png'.	'scimapScatterPlot.png'
**kwargs		Additional keyword arguments to be passed to the matplotlib scatter function.	{}

Returns:

Name	Type	Description
Plot	image	If saveDir is provided the plot will saved within the provided saveDir.

Example

customColors = { 'Unknown' : '#e5e5e5',
                'CD8+ T' : '#ffd166',
                'Non T CD4+ cells' : '#06d6a0',
                'CD4+ T' : '#118ab2',
                'ECAD+' : '#ef476f',
                'Immune' : '#073b4c',
                'KI67+ ECAD+' : '#000000'
    }

sm.pl.spatial_scatterPlot (adata=core6,
                 colorBy = ['ECAD', 'phenotype_gator'],
                 subset = 'unmicst-6_cellMask',
                 figsize=(4,4),
                 s=0.5,
                 plotLegend=True,
                 fontsize=3,
                 dpi=300,
                 vmin=0,
                 vmax=1,
                 customColors=customColors,
                 fileName='scimapScatterPlot.svg',
                 saveDir='/Users/aj/Downloads')

Source code in scimap/plotting/spatial_scatterPlot.py

def spatial_scatterPlot(
    adata,
    colorBy,
    topLayer=None,
    x_coordinate='X_centroid',
    y_coordinate='Y_centroid',
    imageid='imageid',
    layer=None,
    subset=None,
    s=None,
    ncols=None,
    alpha=1,
    dpi=200,
    fontsize=None,
    plotLegend=True,
    cmap='RdBu_r',
    catCmap='tab20',
    vmin=None,
    vmax=None,
    customColors=None,
    figsize=(5, 5),
    invert_yaxis=True,
    saveDir=None,
    fileName='scimapScatterPlot.png',
    **kwargs,
):
    """
    Parameters:
        adata (anndata.AnnData):
            Pass the `adata` loaded into memory or a path to the `adata`
            file (.h5ad).

        colorBy (str):
        The column name that will be used for color-coding the points. This can be
        either markers (data stored in `adata.var`) or observations (data stored in `adata.obs`).

        topLayer (list, optional):
                A list of categories that should be plotted on the top layer. These categories
                must be present in the `colorBy` data. Helps to highlight cell types or cluster that is of interest.

        x_coordinate (str, optional):
            The column name in `spatial feature table` that records the
            X coordinates for each cell.

        y_coordinate (str, optional):
            The column name in `single-cell spatial table` that records the
            Y coordinates for each cell.

        imageid (str, optional):
            The column name in `spatial feature table` that contains the image ID
            for each cell.

        layer (str or None, optional):
            The layer in `adata.layers` that contains the expression data to use.
            If `None`, `adata.X` is used. use `raw` to use the data stored in `adata.raw.X`.

        subset (list or None, optional):
            `imageid` of a single or multiple images to be subsetted for plotting purposes.

        s (float, optional):
            The size of the markers.

        ncols (int, optional):
            The number of columns in the final plot when multiple variables are plotted.

        alpha (float, optional):
            The alpha value of the points (controls opacity).

        dpi (int, optional):
            The DPI of the figure.

        fontsize (int, optional):
            The size of the fonts in plot.

        plotLegend (bool, optional):
            Whether to include a legend.

        cmap (str, optional):
            The colormap to use for continuous data.

        catCmap (str, optional):
            The colormap to use for categorical data.

        vmin (float or None, optional):
            The minimum value of the color scale.

        vmax (float or None, optional):
            The maximum value of the color scale.

        customColors (dict or None, optional):
            A dictionary mapping color categories to colors.

        figsize (tuple, optional):
            The size of the figure. Default is (5, 5).

        invert_yaxis (bool, optional):
            Invert the Y-axis of the plot.

        saveDir (str or None, optional):
            The directory to save the output plot. If None, the plot will not be saved.

        fileName (str, optional):
            The name of the output file. Use desired file format as
            suffix (e.g. `.png` or `.pdf`). Default is 'scimapScatterPlot.png'.

        **kwargs:
            Additional keyword arguments to be passed to the matplotlib scatter function.


    Returns:
        Plot (image):
            If `saveDir` is provided the plot will saved within the
            provided saveDir.

    Example:
            ```python

            customColors = { 'Unknown' : '#e5e5e5',
                            'CD8+ T' : '#ffd166',
                            'Non T CD4+ cells' : '#06d6a0',
                            'CD4+ T' : '#118ab2',
                            'ECAD+' : '#ef476f',
                            'Immune' : '#073b4c',
                            'KI67+ ECAD+' : '#000000'
                }

            sm.pl.spatial_scatterPlot (adata=core6,
                             colorBy = ['ECAD', 'phenotype_gator'],
                             subset = 'unmicst-6_cellMask',
                             figsize=(4,4),
                             s=0.5,
                             plotLegend=True,
                             fontsize=3,
                             dpi=300,
                             vmin=0,
                             vmax=1,
                             customColors=customColors,
                             fileName='scimapScatterPlot.svg',
                             saveDir='/Users/aj/Downloads')


            ```

    """

    # Load the andata object
    if isinstance(adata, str):
        adata = ad.read(adata)
    else:
        adata = adata.copy()

    # subset data if neede
    if subset is not None:
        if isinstance(subset, str):
            subset = [subset]
        if layer == 'raw':
            bdata = adata.copy()
            bdata.X = adata.raw.X
            bdata = bdata[bdata.obs[imageid].isin(subset)]
        else:
            bdata = adata.copy()
            bdata = bdata[bdata.obs[imageid].isin(subset)]
    else:
        bdata = adata.copy()

    # isolate the data
    if layer is None:
        data = pd.DataFrame(bdata.X, index=bdata.obs.index, columns=bdata.var.index)
    elif layer == 'raw':
        data = pd.DataFrame(bdata.raw.X, index=bdata.obs.index, columns=bdata.var.index)
    else:
        data = pd.DataFrame(
            bdata.layers[layer], index=bdata.obs.index, columns=bdata.var.index
        )

    # isolate the meta data
    meta = bdata.obs

    # toplayer logic
    if isinstance(topLayer, str):
        topLayer = [topLayer]

    # identify the things to color
    if isinstance(colorBy, str):
        colorBy = [colorBy]
    # extract columns from data and meta
    data_cols = [col for col in data.columns if col in colorBy]
    meta_cols = [col for col in meta.columns if col in colorBy]
    # combine extracted columns from data and meta
    colorColumns = pd.concat([data[data_cols], meta[meta_cols]], axis=1)

    # identify the x and y coordinates
    x = meta[x_coordinate]
    y = meta[y_coordinate]

    # auto identify rows and columns in the grid plot
    def calculate_grid_dimensions(num_items, num_columns=None):
        """
        Calculates the number of rows and columns for a square grid
        based on the number of items.
        """
        if num_columns is None:
            num_rows_columns = int(math.ceil(math.sqrt(num_items)))
            return num_rows_columns, num_rows_columns
        else:
            num_rows = int(math.ceil(num_items / num_columns))
            return num_rows, num_columns

    # calculate the number of rows and columns
    nrows, ncols = calculate_grid_dimensions(
        len(colorColumns.columns), num_columns=ncols
    )

    # resolve figsize
    # figsize = (figsize[0]*ncols, figsize[1]*nrows)

    # Estimate point size
    if s is None:
        s = (10000 / bdata.shape[0]) / len(colorColumns.columns)

    # Define the categorical colormap (optional)
    cmap_cat = plt.get_cmap(catCmap)

    # FIIGURE
    fig, axs = plt.subplots(nrows=nrows, ncols=ncols, figsize=figsize, dpi=dpi)

    # Flatten the axs array for easier indexing
    if nrows == 1 and ncols == 1:
        axs = [axs]  # wrap single subplot in a list
    else:
        axs = axs.flatten()

    # Loop over the columns of the DataFrame
    for i, col in enumerate(colorColumns):
        # Select the current axis
        ax = axs[i]

        # invert y-axis
        if invert_yaxis is True:
            ax.invert_yaxis()

        # Scatter plot for continuous data
        if colorColumns[col].dtype.kind in 'iufc':
            scatter = ax.scatter(
                x=x,
                y=y,
                c=colorColumns[col],
                cmap=cmap,
                s=s,
                vmin=vmin,
                vmax=vmax,
                linewidths=0,
                alpha=alpha,
                **kwargs,
            )
            if plotLegend is True:
                cbar = plt.colorbar(scatter, ax=ax, pad=0)
                cbar.ax.tick_params(labelsize=fontsize)

        # Scatter plot for categorical data
        else:
            # Get the unique categories in the column
            categories = colorColumns[col].unique()

            # Map the categories to colors using either the custom colors or the categorical colormap
            if customColors:
                colors = {
                    cat: customColors[cat] for cat in categories if cat in customColors
                }
            else:
                colors = {cat: cmap_cat(i) for i, cat in enumerate(categories)}

            # Ensure topLayer categories are plotted last
            categories_to_plot_last = (
                [cat for cat in topLayer if cat in categories] if topLayer else []
            )
            categories_to_plot_first = [
                cat for cat in categories if cat not in categories_to_plot_last
            ]

            # Plot non-topLayer categories first
            for cat in categories_to_plot_first:
                cat_mask = colorColumns[col] == cat
                ax.scatter(
                    x=x[cat_mask],
                    y=y[cat_mask],
                    c=[colors.get(cat, cmap_cat(np.where(categories == cat)[0][0]))],
                    s=s,
                    linewidths=0,
                    alpha=alpha,
                    **kwargs,
                )

            # Then plot topLayer categories
            for cat in categories_to_plot_last:
                cat_mask = colorColumns[col] == cat
                ax.scatter(
                    x=x[cat_mask],
                    y=y[cat_mask],
                    c=[colors.get(cat, cmap_cat(np.where(categories == cat)[0][0]))],
                    s=s,
                    linewidths=0,
                    alpha=alpha,
                    **kwargs,
                )

            if plotLegend is True:
                # Adjust legend to include all categories
                handles = [
                    mpatches.Patch(
                        color=colors.get(
                            cat, cmap_cat(np.where(categories == cat)[0][0])
                        ),
                        label=cat,
                    )
                    for cat in categories
                ]
                ax.legend(
                    handles=handles,
                    bbox_to_anchor=(1.0, 1.0),
                    loc='upper left',
                    bbox_transform=ax.transAxes,
                    fontsize=fontsize,
                )

        ax.set_title(col)  # fontsize=fontsize
        ax.set_yticklabels([])
        ax.set_xticklabels([])
        ax.set_xticks([])
        ax.set_yticks([])

    # Remove any empty subplots
    num_plots = len(colorColumns.columns)
    for i in range(num_plots, nrows * ncols):
        ax = axs[i]
        fig.delaxes(ax)

    # Adjust the layout of the subplots grid
    plt.tick_params(axis='both', labelsize=fontsize)
    plt.tight_layout()

    # save figure
    if saveDir:
        if not os.path.exists(saveDir):
            os.makedirs(saveDir)
        full_path = os.path.join(saveDir, fileName)
        plt.savefig(full_path, dpi=dpi)
        plt.close()
        print(f"Saved plot to {full_path}")
    else:
        plt.show()