adataviz.utils module

class adataviz.utils.TextWithCircleHandler(marker_text='', label_text='', text_kws={}, **kwargs)

Bases: HandlerBase

create_artists(legend, orig_handle, xdescent, ydescent, width, height, fontsize, trans)

Return the legend artists generated.

Parameters:

• legend (~matplotlib.legend.Legend) – The legend for which these legend artists are being created.

• orig_handle (~matplotlib.artist.Artist or similar) – The object for which these legend artists are being created.

• xdescent (int) – The rectangle (xdescent, ydescent, width, height) that the legend artists being created should fit within.

• ydescent (int) – The rectangle (xdescent, ydescent, width, height) that the legend artists being created should fit within.

• width (int) – The rectangle (xdescent, ydescent, width, height) that the legend artists being created should fit within.

• height (int) – The rectangle (xdescent, ydescent, width, height) that the legend artists being created should fit within.

• fontsize (int) – The fontsize in pixels. The legend artists being created should be scaled according to the given fontsize.

• trans (~matplotlib.transforms.Transform) – The transform that is applied to the legend artists being created. Typically from unit coordinates in the handler box to screen coordinates.

adataviz.utils.density_contour(ax, data, x, y, groupby=None, c='lightgray', single_contour_pad=1, linewidth=1, palette=None)

adataviz.utils.despine(fig=None, ax=None, top=True, right=True, left=False, bottom=False)

Remove the top and right spines from plot(s).

Parameters:

• fig (matplotlib figure, optional) – Figure to despine all axes of, defaults to the current figure.

• ax (matplotlib axes, optional) – Specific axes object to despine. Ignored if fig is provided.

• top (boolean, optional) – If True, remove that spine.

• right (boolean, optional) – If True, remove that spine.

• left (boolean, optional) – If True, remove that spine.

• bottom (boolean, optional) – If True, remove that spine.

Return type:

None

adataviz.utils.df2stdout(df)

adataviz.utils.get_brain_region_structure()

https://atlas.brain-map.org/ BICAN: https://atlas.brain-map.org/atlasviewer/ontologies/11.json HBA: https://atlas.brain-map.org/atlasviewer/ontologies/7.json

adataviz.utils.level_one_palette(name_list, order=None, palette='auto')

adataviz.utils.mpl_style()

adataviz.utils.normalize_mc_by_cell(use_adata, normalize_per_cell=True, clip_norm_value=10, verbose=1, hypo_score=False)

adataviz.utils.parse_gtf(gtf='gencode.v43.annotation.gtf', outfile=None)

adataviz.utils.parse_json(url)

adataviz.utils.plot_cmap_legend(cax=None, ax=None, cmap='turbo', label=None, kws=None, labelsize=6, linewidth=0.5, ticklabel_size=4)

Plot legend for cmap.

Parameters:

• cax (Axes into which the colorbar will be drawn.)

• ax (axes to anchor.)

• cmap (turbo, hsv, Set1, Dark2, Paired, Accent,tab20,exp1,exp2,meth1,meth2)

• label (title for legend.)

• kws (dict) – kws passed to plt.colorbar (matplotlib.figure.Figure.colorbar).

Returns:

cbar

Return type:

axes of legend

adataviz.utils.plot_color_dict_legend(D, ax=None, title=None, color_text=True, kws=None, luminance=0.5)

plot legned for color dict

Parameters:

• D (a dict, key is categorical variable, values are colors.)

• ax (axes to plot the legend.)

• title (title of legend.)

• color_text (whether to change the color of text based on the color in D.)

• label_side (right of left.)

• kws (kws passed to plt.legend.)

Return type:

ax.legend

adataviz.utils.plot_marker_legend(color_dict=None, ax=None, title=None, color_text=True, marker='o', kws=None, luminance=0.5)

plot legned for different marker

Parameters:

• D (a dict, key is categorical variable, values are marker.)

• ax (axes to plot the legend.)

• title (title of legend.)

• color_text (whether to change the color of text based on the color in D.)

• label_side (right of left.)

• kws (kws passed to plt.legend.)

Return type:

ax.legend

adataviz.utils.plot_text_legend(color_dict, code2label, ax=None, title=None, color_text=True, boxstyle='Circle', marker_pad=0.1, legend_kws=None, marker_fontsize=4, text_kws=None, alpha=0.7, luminance=0.5)

adataviz.utils.prepare_color_palette(color_dict=None, outpath='palette.xlsx')

Generating a .xlsx file including all color palette.

Parameters:

colors (dict) – A dict of dict, keys are categorical terms, values are HEX color code

adataviz.utils.read_google_sheet(url=None, **kwargs)

adataviz.utils.serialize(x)

adataviz.utils.tight_hue_range(hue_data, portion)

Automatic select a SMALLEST data range that covers [portion] of the data.

adataviz.utils.zoom_ax(ax, zoom_scale, on='both')

Zoom ax on both x and y-axis.

adataviz.utils.zoom_min_max(vmin, vmax, scale)

Zoom min and max value.