Merge pull request #12 from berberto/main

Fixed color range and added `show_cbar` option in `plot_swanson_vector`

iblatlas/plots.py

@@ -828,7 +828,8 @@ def plot_scalar_on_barplot(acronyms, values, errors=None, order=True, ax=None, b
 
 def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br=None, orientation='landscape',
                         empty_color='silver', vmin=None, vmax=None, cmap='viridis', annotate=False, annotate_n=10,
-                        annotate_order='top', annotate_list=None, mask=None, mask_color='w', fontsize=10, **kwargs):
+                        annotate_order='top', annotate_list=None, mask=None, mask_color='w', fontsize=10,
+                        show_cbar=False, extend='neither', **kwargs):
     """
     Function to plot scalar value per allen region on the swanson projection. Plots on a vecortised version of the
     swanson projection
@@ -854,8 +855,12 @@ def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br
         Minimum value to restrict the colormap
     vmax: float
         Maximum value to restrict the colormap
-    cmap: string
-        matplotlib named colormap to use
+    cmap: string or matplotlib.colors.Colormap
+        matplotlib colormap to use
+    show_cbar: bool, default=False
+        Whether to display a colorbar.
+    extend: str, default='neither'
+        Which side of the colorbar to extend. See `colorbar` documentation.
     annotate : bool, default=False
         If true, labels the regions with acronyms.
     annotate_n: int
@@ -886,6 +891,8 @@ def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br
     if ax is None:
         fig, ax = plt.subplots()
         ax.set_axis_off()
+    else:
+        fig = ax.get_figure()
 
     if hemisphere != 'both' and acronyms is not None and not isinstance(acronyms[0], str):
         # If negative atlas ids are passed in and we are not going to lateralise (e.g hemisphere='both')
@@ -894,11 +901,22 @@ def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br
 
     if acronyms is not None:
         ibr, vals = br.propagate_down(acronyms, values)
-        colormap = matplotlib.colormaps.get_cmap(cmap)
-        vmin = vmin or np.nanmin(vals)
-        vmax = vmax or np.nanmax(vals)
+
+        if isinstance(cmap, matplotlib.colors.Colormap):
+            colormap = cmap
+        elif isinstance(cmap, str):
+            colormap = matplotlib.colormaps.get_cmap(cmap)
+        else:
+            raise ValueError("`cmap` option must be of type `str` or `matplotlib.colors.Colormap`")
+
+        vmin = vmin if vmin is not None else np.nanmin(vals)
+        vmax = vmax if vmax is not None else np.nanmax(vals)
         norm = colors.Normalize(vmin=vmin, vmax=vmax)
         rgba_color = colormap(norm(vals), bytes=True)
+        if show_cbar:
+            fig.colorbar(cm.ScalarMappable(norm=norm, cmap=cmap),
+                         ax=ax, orientation='vertical', extend=extend,
+                         )
 
     if mask is not None:
         imr, _ = br.propagate_down(mask, np.ones_like(mask))