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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

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1 watching

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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" + '
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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

Watchers

1 watching

Forks

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Contributors

Languages

, '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('^' + ".*" + '
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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

Watchers

1 watching

Forks

Releases

Packages

Contributors

Languages

, '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('^' + ".*" + '
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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

Watchers

1 watching

Forks

Releases

Packages

Contributors

Languages

, '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" + '
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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

Watchers

1 watching

Forks

Releases

Packages

Contributors

Languages

, '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('^' + ".*" + '
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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

Watchers

1 watching

Forks

Releases

Packages

Contributors

Languages

, '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('^' + ".*" + '
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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

Watchers

1 watching

Forks

Releases

Packages

Contributors

Languages

, '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); } })(); })();
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plotgistic

Scripts to create nice gistic visualisations.

Please excuse the bad coding, and light documentation!

Prerequisites

  • Developed using perl v5.26.1 built for x86_64-linux-gnu-thread-multi
  • Developed using R v3.6.1 built for x86_64-conda_cos6-linux-gnu
  • AFAIK no special libraries are required so this should work on any perl v5.x.x and R v3.x.x

Usage

First run gistic2.0 (this is tested on the output of gistic 2.0.23)

Preprocess data

First create a table that will be used for the plotting script:

perl gistic_2_dataframe_for_plotting.pl scores.gistic del_genes.conf_20.txt amp_genes.conf_20.txt > myProject_gistic_table.tsv

Plot

Create the plot:

R -f plot_gistic_table.r --args myProject_gistic_table.tsv
display myProject_gistic_table.tsv.pdf

Plot with custom genes

Create the plot, but adding in other genes that you are interested in (in a 4 column BED file, no chr prefix, and 4th column is the name)

R -f plot_gistic_table.r --args myProject_gistic_table.tsv my_favourite_genes.bed

If you want to change the genes reported by gistic, find the lines with "Gene_amp" and "Gene_del", and modify the column with the gene names

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Naveed Ishaque

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

Dorett I Odoni

About

scripts to create nice gistic visualisations

Resources

Stars

1 star

Watchers

1 watching

Forks

Releases

Packages

Contributors

Languages