{ "schemaVersion": "1.0", "item": { "slug": "generating-publication-ready-figures-in-r", "name": "Generating Publication Ready Figures In R", "source": "tencent", "type": "skill", "category": "数据分析", "sourceUrl": "https://clawhub.ai/JackKuo666/generating-publication-ready-figures-in-r", "canonicalUrl": "https://clawhub.ai/JackKuo666/generating-publication-ready-figures-in-r", "targetPlatform": "OpenClaw" }, "install": { "downloadMode": "redirect", "downloadUrl": "/downloads/generating-publication-ready-figures-in-r", "sourceDownloadUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=generating-publication-ready-figures-in-r", "sourcePlatform": "tencent", "targetPlatform": "OpenClaw", "installMethod": "Manual import", "extraction": "Extract archive", "prerequisites": [ "OpenClaw" ], "packageFormat": "ZIP package", "includedAssets": [ "README.md", "SKILL.md" ], "primaryDoc": "SKILL.md", "quickSetup": [ "Download the package from Yavira.", "Extract the archive and review SKILL.md first.", "Import or place the package into your OpenClaw setup." ], "agentAssist": { "summary": "Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.", "steps": [ "Download the package from Yavira.", "Extract it into a folder your agent can access.", "Paste one of the prompts below and point your agent at the extracted folder." ], "prompts": [ { "label": "New install", "body": "I downloaded a skill package from Yavira. 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Summarize what changed and any follow-up checks I should run." } ] }, "documentation": { "source": "clawhub", "primaryDoc": "SKILL.md", "sections": [ { "title": "Generating Publication-Ready Figures in R", "body": "This skill specializes in transforming ordinary ggplot2 plots into professional, publication-ready figures that meet the strict standards of top-tier journals like Nature, Science, Cell, and others.\n\nUse this skill when the user wants to:\n\nConvert ggplot plots to journal-style figures\nApply Nature/Science publication themes to existing plots\nCreate multi-panel figures with consistent styling\nExport figures with proper DPI, dimensions, and formats\nMatch specific journal submission guidelines\nCreate colorblind-safe and publication-quality color schemes" }, { "title": "What This Skill Does", "body": "When activated, this skill will:\n\nAnalyze existing ggplot code - Read and understand the current plot structure\n\n\nApply journal themes - Add publication-quality themes including:\n\nProper font sizes and families\nClean axis lines and backgrounds\nJournal-specific color palettes\nLegend positioning and styling\n\n\n\nOptimize for submission - Ensure figures meet:\n\nDPI requirements (typically 300-600 DPI)\nWidth/height specifications (single vs double column)\nFile format requirements (TIFF, PDF, EPS)\nColor space requirements (CMYK vs RGB)\n\n\n\nCreate multi-panel figures - Combine plots using:\n\npatchwork for simple layouts\ncowplot for complex compositions\nCustom annotation and labeling\n\n\n\nExport properly - Save with correct:\n\nResolution (DPI)\nDimensions (inches/cm)\nFile format\nColor profile" }, { "title": "Example User Requests That Should Trigger This Skill", "body": "\"Transform this ggplot to Nature journal style\"\n\"Make this figure publication-ready for Science\"\n\"Create a two-column figure matching Cell format\"\n\"Export these plots at 600 DPI for submission\"\n\"Apply a colorblind-safe palette to my plots\"\n\"Combine these four plots into one publication figure\"\n\"Format my scatter plot for PNAS submission\"" }, { "title": "Nature Style", "body": "Font: Arial or Helvetica\nFont sizes: Axis titles 7-9 pt, axis labels 6-8 pt\nSingle column: 89 mm (3.5 in) width\nDouble column: 183 mm (7.2 in) width\nMax height: 234 mm (9.2 in)\nResolution: 300-600 DPI\nFormats: TIFF, PDF, EPS (vector preferred)" }, { "title": "Science Style", "body": "Font: Arial\nFont sizes: Title 9 pt, labels 7 pt\nSingle column: 57 mm (2.25 in) width\nDouble column: 114 mm (4.5 in) width\nResolution: 300-600 DPI\nFormats: TIFF, PDF, EPS" }, { "title": "Cell Press Style", "body": "Font: Arial or Helvetica\nSingle column: 85 mm (3.3 in) width\nDouble column: 178 mm (7 in) width\nResolution: 300 DPI minimum\nFormats: TIFF, EPS, PDF" }, { "title": "theme_nature()", "body": "Clean, minimalist theme matching Nature journals:\n\nNo gray backgrounds\nMinimal grid lines\nArial font family\nProper axis sizing" }, { "title": "theme_science()", "body": "Theme for Science journal submissions:\n\nCompact layout\nClean typography\nOptimized for smaller widths" }, { "title": "theme_cellpress()", "body": "Cell Press journal theme:\n\nProfessional appearance\nFlexible legend placement\nPublication-ready defaults" }, { "title": "theme_colorblind()", "body": "Colorblind-safe palette with:\n\nViridis/Colorbrewer schemes\nHigh contrast ratios\nPrint-friendly colors" }, { "title": "Nature-Approved Colors", "body": "# Primary colors\nnature_colors <- c(\n blue = \"#3B4992\",\n red = \"#EE0000\",\n green = \"#008B45\",\n purple = \"#631879\"\n)" }, { "title": "Colorblind-Safe Scales", "body": "scale_fill_viridis()\nscale_color_okabe_ito() (Okabe-Ito palette)\nscale_color_viridis()" }, { "title": "Example Workflow", "body": "User: Here's my ggplot code, make it Nature-style.\n\n# Original plot\np <- ggplot(mtcars, aes(x = wt, y = mpg, color = factor(cyl))) +\n geom_point(size = 3)\n\nSkill transforms to:\n\n# Publication-ready version\np <- ggplot(mtcars, aes(x = \"Weight (tons)\", y = \"Fuel Efficiency (mpg)\",\n color = \"Cylinders\")) +\n geom_point(size = 2.5, shape = 16, alpha = 0.8) +\n scale_color_nature() +\n theme_nature(base_size = 8) +\n labs(title = NULL)\n\n# Export at correct size\nggsave(\"figure1.pdf\", p, width = 3.5, height = 3, dpi = 300,\n device = \"pdf\")" }, { "title": "Multi-Panel Figures", "body": "# Combine plots with patchwork\nlibrary(patchwork)\n\nfigure1 <- (panel_a | panel_b) / (panel_c | panel_d)\n\n# Add panel labels\nfigure1 <- figure1 +\n plot_annotation(tag_levels = \"A\",\n tag_suffix = \")\")\n\n# Export\nggsave(\"figure1.pdf\", figure1, width = 7, height = 6, dpi = 300)" }, { "title": "Tools & Packages Commonly Used", "body": "PurposeR PackagesBase plottingggplot2Themesggplot2, cowplot, hrbrthemesColor palettesviridis, RColorBrewer, scales, ggsciMulti-panelpatchwork, cowplot, ggpubrExportggplot2, raggFontsextrafont, showtextAnnotationsggrepel, ggpp" }, { "title": "Common Journal Requirements", "body": "JournalWidth (single)Width (double)Max HeightMin DPINature89 mm183 mm234 mm300Science57 mm114 mm229 mm300Cell85 mm178 mm229 mm300PNAS87 mm178 mm227 mm300PLOS ONE170 mm-230 mm300eLife183 mm-244 mm300" }, { "title": "Applying a theme", "body": "p + theme_nature() # Nature style\np + theme_science() # Science style\np + theme_cellpress() # Cell Press style\np + theme_colorblind() # Colorblind-safe" }, { "title": "Export formats", "body": "# Vector (preferred)\nggsave(\"figure.pdf\", ... device = \"pdf\")\nggsave(\"figure.eps\", ... device = \"eps\")\n\n# Raster (high DPI)\nggsave(\"figure.tiff\", ... device = \"tiff\", dpi = 600)\nggsave(\"figure.png\", ... device = \"png\", dpi = 300)" }, { "title": "Common fixes", "body": "Text too small: Increase base_size in theme\nLegend overlap: Use theme(legend.position = \"bottom\")\nColors not distinct: Use scale_fill_viridis()\nFonts not rendering: Use extrafont::font_import()" }, { "title": "Notes", "body": "Always check specific journal guidelines before submission\nVector formats (PDF/EPS) are preferred over raster\nUse consistent styling across all figures in a paper\nTest colorblind accessibility with colorblindr package\nKeep axis labels clear and concise\nAvoid redundant chart junk (backgrounds, grid lines)" } ], "body": "Generating Publication-Ready Figures in R\n\nThis skill specializes in transforming ordinary ggplot2 plots into professional, publication-ready figures that meet the strict standards of top-tier journals like Nature, Science, Cell, and others.\n\nUse this skill when the user wants to:\n\nConvert ggplot plots to journal-style figures\nApply Nature/Science publication themes to existing plots\nCreate multi-panel figures with consistent styling\nExport figures with proper DPI, dimensions, and formats\nMatch specific journal submission guidelines\nCreate colorblind-safe and publication-quality color schemes\nWhat This Skill Does\n\nWhen activated, this skill will:\n\nAnalyze existing ggplot code - Read and understand the current plot structure\n\nApply journal themes - Add publication-quality themes including:\n\nProper font sizes and families\nClean axis lines and backgrounds\nJournal-specific color palettes\nLegend positioning and styling\n\nOptimize for submission - Ensure figures meet:\n\nDPI requirements (typically 300-600 DPI)\nWidth/height specifications (single vs double column)\nFile format requirements (TIFF, PDF, EPS)\nColor space requirements (CMYK vs RGB)\n\nCreate multi-panel figures - Combine plots using:\n\npatchwork for simple layouts\ncowplot for complex compositions\nCustom annotation and labeling\n\nExport properly - Save with correct:\n\nResolution (DPI)\nDimensions (inches/cm)\nFile format\nColor profile\nExample User Requests That Should Trigger This Skill\n\"Transform this ggplot to Nature journal style\"\n\"Make this figure publication-ready for Science\"\n\"Create a two-column figure matching Cell format\"\n\"Export these plots at 600 DPI for submission\"\n\"Apply a colorblind-safe palette to my plots\"\n\"Combine these four plots into one publication figure\"\n\"Format my scatter plot for PNAS submission\"\nJournal Style Guidelines\nNature Style\nFont: Arial or Helvetica\nFont sizes: Axis titles 7-9 pt, axis labels 6-8 pt\nSingle column: 89 mm (3.5 in) width\nDouble column: 183 mm (7.2 in) width\nMax height: 234 mm (9.2 in)\nResolution: 300-600 DPI\nFormats: TIFF, PDF, EPS (vector preferred)\nScience Style\nFont: Arial\nFont sizes: Title 9 pt, labels 7 pt\nSingle column: 57 mm (2.25 in) width\nDouble column: 114 mm (4.5 in) width\nResolution: 300-600 DPI\nFormats: TIFF, PDF, EPS\nCell Press Style\nFont: Arial or Helvetica\nSingle column: 85 mm (3.3 in) width\nDouble column: 178 mm (7 in) width\nResolution: 300 DPI minimum\nFormats: TIFF, EPS, PDF\nTheme Templates Available\ntheme_nature()\n\nClean, minimalist theme matching Nature journals:\n\nNo gray backgrounds\nMinimal grid lines\nArial font family\nProper axis sizing\ntheme_science()\n\nTheme for Science journal submissions:\n\nCompact layout\nClean typography\nOptimized for smaller widths\ntheme_cellpress()\n\nCell Press journal theme:\n\nProfessional appearance\nFlexible legend placement\nPublication-ready defaults\ntheme_colorblind()\n\nColorblind-safe palette with:\n\nViridis/Colorbrewer schemes\nHigh contrast ratios\nPrint-friendly colors\nColor Palettes\nNature-Approved Colors\n# Primary colors\nnature_colors <- c(\n blue = \"#3B4992\",\n red = \"#EE0000\",\n green = \"#008B45\",\n purple = \"#631879\"\n)\n\nColorblind-Safe Scales\nscale_fill_viridis()\nscale_color_okabe_ito() (Okabe-Ito palette)\nscale_color_viridis()\nExample Workflow\n\nUser: Here's my ggplot code, make it Nature-style.\n\n# Original plot\np <- ggplot(mtcars, aes(x = wt, y = mpg, color = factor(cyl))) +\n geom_point(size = 3)\n\n\nSkill transforms to:\n\n# Publication-ready version\np <- ggplot(mtcars, aes(x = \"Weight (tons)\", y = \"Fuel Efficiency (mpg)\",\n color = \"Cylinders\")) +\n geom_point(size = 2.5, shape = 16, alpha = 0.8) +\n scale_color_nature() +\n theme_nature(base_size = 8) +\n labs(title = NULL)\n\n# Export at correct size\nggsave(\"figure1.pdf\", p, width = 3.5, height = 3, dpi = 300,\n device = \"pdf\")\n\nMulti-Panel Figures\n# Combine plots with patchwork\nlibrary(patchwork)\n\nfigure1 <- (panel_a | panel_b) / (panel_c | panel_d)\n\n# Add panel labels\nfigure1 <- figure1 +\n plot_annotation(tag_levels = \"A\",\n tag_suffix = \")\")\n\n# Export\nggsave(\"figure1.pdf\", figure1, width = 7, height = 6, dpi = 300)\n\nTools & Packages Commonly Used\nPurpose\tR Packages\nBase plotting\tggplot2\nThemes\tggplot2, cowplot, hrbrthemes\nColor palettes\tviridis, RColorBrewer, scales, ggsci\nMulti-panel\tpatchwork, cowplot, ggpubr\nExport\tggplot2, ragg\nFonts\textrafont, showtext\nAnnotations\tggrepel, ggpp\nCommon Journal Requirements\nJournal\tWidth (single)\tWidth (double)\tMax Height\tMin DPI\nNature\t89 mm\t183 mm\t234 mm\t300\nScience\t57 mm\t114 mm\t229 mm\t300\nCell\t85 mm\t178 mm\t229 mm\t300\nPNAS\t87 mm\t178 mm\t227 mm\t300\nPLOS ONE\t170 mm\t-\t230 mm\t300\neLife\t183 mm\t-\t244 mm\t300\nQuick Reference\nApplying a theme\np + theme_nature() # Nature style\np + theme_science() # Science style\np + theme_cellpress() # Cell Press style\np + theme_colorblind() # Colorblind-safe\n\nExport formats\n# Vector (preferred)\nggsave(\"figure.pdf\", ... device = \"pdf\")\nggsave(\"figure.eps\", ... device = \"eps\")\n\n# Raster (high DPI)\nggsave(\"figure.tiff\", ... device = \"tiff\", dpi = 600)\nggsave(\"figure.png\", ... device = \"png\", dpi = 300)\n\nCommon fixes\nText too small: Increase base_size in theme\nLegend overlap: Use theme(legend.position = \"bottom\")\nColors not distinct: Use scale_fill_viridis()\nFonts not rendering: Use extrafont::font_import()\nNotes\nAlways check specific journal guidelines before submission\nVector formats (PDF/EPS) are preferred over raster\nUse consistent styling across all figures in a paper\nTest colorblind accessibility with colorblindr package\nKeep axis labels clear and concise\nAvoid redundant chart junk (backgrounds, grid lines)" }, "trust": { "sourceLabel": "tencent", "provenanceUrl": "https://clawhub.ai/JackKuo666/generating-publication-ready-figures-in-r", "publisherUrl": "https://clawhub.ai/JackKuo666/generating-publication-ready-figures-in-r", "owner": "JackKuo666", "version": "0.1.0", "license": null, "verificationStatus": "Indexed source record" }, "links": { "detailUrl": "https://openagent3.xyz/skills/generating-publication-ready-figures-in-r", "downloadUrl": "https://openagent3.xyz/downloads/generating-publication-ready-figures-in-r", "agentUrl": "https://openagent3.xyz/skills/generating-publication-ready-figures-in-r/agent", "manifestUrl": "https://openagent3.xyz/skills/generating-publication-ready-figures-in-r/agent.json", "briefUrl": "https://openagent3.xyz/skills/generating-publication-ready-figures-in-r/agent.md" } }