To do #1

Open
Open
To do#1

Description

@jhcreed
jhcreed
opened on Dec 4, 2020

Content team

Page one - tumor level:

  • spatial plots color coding points by positivity
  • summary plots of distributions of markers
  • ripleys K plots (along various values of R)

Page two - study level:

  • violin plots of overall distributions
  • heatmaps with clinical annotations
  • distributions by clinical characteristics

Shiny team

  • page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
  • page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
  • page three - readme/help info
  • custom css

Shiny tutorials :
https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
https://deanattali.com/blog/building-shiny-apps-tutorial/

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      , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
       blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n 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;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

      Skip to content
      To do #1
      Open
      Open
      To do#1
      Description
      @jhcreed
      jhcreed
      opened on Dec 4, 2020
      Content team
      Page one - tumor level:
      •  spatial plots color coding points by positivity
      •  summary plots of distributions of markers
      •  ripleys K plots (along various values of R)
      Page two - study level:
      •  violin plots of overall distributions
      •  heatmaps with clinical annotations
      •  distributions by clinical characteristics
      Shiny team
      •  page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
      •  page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
      •  page three - readme/help info
      •  custom css
      Shiny tutorials :
      https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
      https://deanattali.com/blog/building-shiny-apps-tutorial/
      Metadata
      Metadata
      Assignees
      No one assigned
        Labels
        No labels
        No labels
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        No type
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        No projects
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          No milestone
          Relationships
          None yet
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          No branches or pull requests
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

          Skip to content
          To do #1
          Open
          Open
          To do#1
          Description
          @jhcreed
          jhcreed
          opened on Dec 4, 2020
          Content team
          Page one - tumor level:
          •  spatial plots color coding points by positivity
          •  summary plots of distributions of markers
          •  ripleys K plots (along various values of R)
          Page two - study level:
          •  violin plots of overall distributions
          •  heatmaps with clinical annotations
          •  distributions by clinical characteristics
          Shiny team
          •  page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
          •  page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
          •  page three - readme/help info
          •  custom css
          Shiny tutorials :
          https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
          https://deanattali.com/blog/building-shiny-apps-tutorial/
          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)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

              Skip to content
              To do #1
              Open
              Open
              To do#1
              Description
              @jhcreed
              jhcreed
              opened on Dec 4, 2020
              Content team
              Page one - tumor level:
              •  spatial plots color coding points by positivity
              •  summary plots of distributions of markers
              •  ripleys K plots (along various values of R)
              Page two - study level:
              •  violin plots of overall distributions
              •  heatmaps with clinical annotations
              •  distributions by clinical characteristics
              Shiny team
              •  page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
              •  page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
              •  page three - readme/help info
              •  custom css
              Shiny tutorials :
              https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
              https://deanattali.com/blog/building-shiny-apps-tutorial/
              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)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

                  Skip to content
                  To do #1
                  Open
                  Open
                  To do#1
                  Description
                  @jhcreed
                  jhcreed
                  opened on Dec 4, 2020
                  Content team
                  Page one - tumor level:
                  •  spatial plots color coding points by positivity
                  •  summary plots of distributions of markers
                  •  ripleys K plots (along various values of R)
                  Page two - study level:
                  •  violin plots of overall distributions
                  •  heatmaps with clinical annotations
                  •  distributions by clinical characteristics
                  Shiny team
                  •  page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
                  •  page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
                  •  page three - readme/help info
                  •  custom css
                  Shiny tutorials :
                  https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
                  https://deanattali.com/blog/building-shiny-apps-tutorial/
                  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)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                      Skip to content
                      To do #1
                      Open
                      Open
                      To do#1
                      Description
                      @jhcreed
                      jhcreed
                      opened on Dec 4, 2020
                      Content team
                      Page one - tumor level:
                      •  spatial plots color coding points by positivity
                      •  summary plots of distributions of markers
                      •  ripleys K plots (along various values of R)
                      Page two - study level:
                      •  violin plots of overall distributions
                      •  heatmaps with clinical annotations
                      •  distributions by clinical characteristics
                      Shiny team
                      •  page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
                      •  page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
                      •  page three - readme/help info
                      •  custom css
                      Shiny tutorials :
                      https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
                      https://deanattali.com/blog/building-shiny-apps-tutorial/
                      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)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                          Skip to content
                          To do #1
                          Open
                          Open
                          To do#1
                          Description
                          @jhcreed
                          jhcreed
                          opened on Dec 4, 2020
                          Content team
                          Page one - tumor level:
                          •  spatial plots color coding points by positivity
                          •  summary plots of distributions of markers
                          •  ripleys K plots (along various values of R)
                          Page two - study level:
                          •  violin plots of overall distributions
                          •  heatmaps with clinical annotations
                          •  distributions by clinical characteristics
                          Shiny team
                          •  page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
                          •  page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
                          •  page three - readme/help info
                          •  custom css
                          Shiny tutorials :
                          https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
                          https://deanattali.com/blog/building-shiny-apps-tutorial/
                          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)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

                              Skip to content
                              To do #1
                              Open
                              Open
                              To do#1
                              Description
                              @jhcreed
                              jhcreed
                              opened on Dec 4, 2020
                              Content team
                              Page one - tumor level:
                              •  spatial plots color coding points by positivity
                              •  summary plots of distributions of markers
                              •  ripleys K plots (along various values of R)
                              Page two - study level:
                              •  violin plots of overall distributions
                              •  heatmaps with clinical annotations
                              •  distributions by clinical characteristics
                              Shiny team
                              •  page one - plot color picker, plotly - only show certain types of cells, pick summary plots (only cd3, all, tumor ...), ripleys k - choose edge correction
                              •  page two - heatmap cluster columns/rows/neither , violin plots by clinical characteristics
                              •  page three - readme/help info
                              •  custom css
                              Shiny tutorials :
                              https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/
                              https://deanattali.com/blog/building-shiny-apps-tutorial/
                              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