Skip to content

Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687

Closed
Closed
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687

Description

@timtreis
timtreis
opened on May 28, 2026

Problem

In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.

This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.

Root cause

_draw_colorbar in pl/basic.py places the colorbar with:

cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)

i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.

How scanpy avoids this

scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:

  • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
  • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space: 
    box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])

Proposed fix

Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.

Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).

Discovered while implementing #611 (multi-panel color=[...]).

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions

      , 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
       blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots · Issue #687 · scverse/spatialdata-plot · GitHub
      Skip to content
      Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687
      Closed
      Closed
      Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687
      Description
      @timtreis
      timtreis
      opened on May 28, 2026
      Problem
      In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.
      This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.
      Root cause
      _draw_colorbar in pl/basic.py places the colorbar with:
      cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)
      i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.
      How scanpy avoids this
      scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:
      • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
      • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space:

        box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])
      Proposed fix
      Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.
      Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).
      Discovered while implementing #611 (multi-panel color=[...]).
      Metadata
      Metadata
      Assignees
      No one assigned
        Labels
        No labels
        No labels
        Type
        No type
        Projects
        No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots · Issue #687 · scverse/spatialdata-plot · GitHub
          Skip to content
          Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687
          Closed
          Closed
          Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687
          Description
          @timtreis
          timtreis
          opened on May 28, 2026
          Problem
          In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.
          This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.
          Root cause
          _draw_colorbar in pl/basic.py places the colorbar with:
          cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)
          i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.
          How scanpy avoids this
          scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:
          • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
          • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space:

            box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])
          Proposed fix
          Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.
          Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).
          Discovered while implementing #611 (multi-panel color=[...]).
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots · Issue #687 · scverse/spatialdata-plot · GitHub
              Skip to content
              Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687
              Closed
              Closed
              Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687
              Description
              @timtreis
              timtreis
              opened on May 28, 2026
              Problem
              In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.
              This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.
              Root cause
              _draw_colorbar in pl/basic.py places the colorbar with:
              cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)
              i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.
              How scanpy avoids this
              scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:
              • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
              • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space:

                box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])
              Proposed fix
              Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.
              Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).
              Discovered while implementing #611 (multi-panel color=[...]).
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                No labels
                No labels
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions
                  
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots · Issue #687 · scverse/spatialdata-plot · GitHub
                  Skip to content
                  Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687
                  Closed
                  Closed
                  Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687
                  Description
                  @timtreis
                  timtreis
                  opened on May 28, 2026
                  Problem
                  In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.
                  This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.
                  Root cause
                  _draw_colorbar in pl/basic.py places the colorbar with:
                  cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)
                  i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.
                  How scanpy avoids this
                  scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:
                  • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
                  • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space:

                    box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])
                  Proposed fix
                  Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.
                  Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).
                  Discovered while implementing #611 (multi-panel color=[...]).
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
                    No labels
                    No labels
                    Type
                    No type
                    Projects
                    No projects
                      Milestone
                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots · Issue #687 · scverse/spatialdata-plot · GitHub
                      Skip to content
                      Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687
                      Closed
                      Closed
                      Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687
                      Description
                      @timtreis
                      timtreis
                      opened on May 28, 2026
                      Problem
                      In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.
                      This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.
                      Root cause
                      _draw_colorbar in pl/basic.py places the colorbar with:
                      cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)
                      i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.
                      How scanpy avoids this
                      scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:
                      • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
                      • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space:

                        box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])
                      Proposed fix
                      Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.
                      Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).
                      Discovered while implementing #611 (multi-panel color=[...]).
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
                          Relationships
                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots · Issue #687 · scverse/spatialdata-plot · GitHub
                          Skip to content
                          Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687
                          Closed
                          Closed
                          Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687
                          Description
                          @timtreis
                          timtreis
                          opened on May 28, 2026
                          Problem
                          In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.
                          This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.
                          Root cause
                          _draw_colorbar in pl/basic.py places the colorbar with:
                          cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)
                          i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.
                          How scanpy avoids this
                          scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:
                          • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
                          • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space:

                            box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])
                          Proposed fix
                          Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.
                          Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).
                          Discovered while implementing #611 (multi-panel color=[...]).
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
                            Projects
                            No projects
                              Milestone
                              No milestone
                              Relationships
                              None yet
                              Development
                              No branches or pull requests
                              Issue actions
                              
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots · Issue #687 · scverse/spatialdata-plot · GitHub
                              Skip to content
                              Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots #687
                              Closed
                              Closed
                              Per-panel colorbars/legends overflow into neighbouring panels in multi-panel plots#687
                              Description
                              @timtreis
                              timtreis
                              opened on May 28, 2026
                              Problem
                              In multi-panel figures (multiple coordinate systems, or scanpy-style color=[...]), each panel's colorbar/legend is drawn outside the panel via inset_axes anchored to the right of ax.transAxes. When panels get small (grids, constrained canvases), the colorbar/legend — and especially its tick labels — spill into the adjacent panel.
                              This is most visible when several panels each carry their own colorbar (continuous) or legend (categorical): the left panel's colorbar collides with the right panel's y-axis labels.
                              Root cause
                              _draw_colorbar in pl/basic.py places the colorbar with:
                              cax=inset_axes(spec.ax, ..., bbox_to_anchor=(1+pad, 0, fraction, 1), bbox_transform=spec.ax.transAxes)
                              i.e. outside the panel's cell. No layout engine reserves that space, so it overflows the neighbour. Categorical legends are similarly placed in the right margin.
                              How scanpy avoids this
                              scanpy reserves the colorbar/legend space inside each panel's own cell (steals from the axes), so it can never overflow:
                              • Continuous: plt.colorbar(cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=...) — ax=ax shrinks the panel and places the colorbar in the reclaimed space.
                              • Categorical (multi-panel): shrink the axis first, then add the legend in the freed space:

                                box=ax.get_position(); ax.set_position([box.x0, box.y0, box.width*0.91, box.height])
                              Proposed fix
                              Switch the colorbar subsystem to space-stealing plt.colorbar(ax=ax, location=, fraction=, pad=) and adopt the shrink-then-place pattern for categorical legends. This makes both single- and multi-panel layouts robust at any figure size.
                              Note: library-wide rendering change — affects every colorbar/legend and requires regenerating a large set of visual baselines. Preserve the existing public knobs (location left/right/top/bottom, colorbar_params, same-side stacking, alpha, label).
                              Discovered while implementing #611 (multi-panel color=[...]).
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
                                Type
                                No type
                                Projects
                                No projects
                                  Milestone
                                  No milestone
                                  Relationships
                                  None yet
                                  Development
                                  No branches or pull requests
                                  Issue actions