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"ggtext::element_markdown", "ggplot2::theme_void", "ggplot2::ggsave" ], "pinnedReferences": [], "verification": { "passed": true, "identicalPixels": true, "tiffRgb": true, "tiffLzw": true, "dimensions": [ 2716, 2598 ], "codeSha256": "280d8caffbf9e3b47edefa786233fafa38336f9cd0fda2b6f3cac1c35e87e404", "executableSha256": "1cab1b595af6e10e2cfa41dbc33312ad5d3a65c358e5c0fdfb624be551415cb1", "verifiedCodeSha256": "280d8caffbf9e3b47edefa786233fafa38336f9cd0fda2b6f3cac1c35e87e404", "commentOnlyUpdate": false, "warnings": [] } }, "nc2020-expression-embedding": { "id": "nc2020-expression-embedding", "sourceIds": [ "6db78d2d0c7f4c17", "bf751dde7ad7a861" ], "conditions": "同论文Fig.6b，连续蓝—浅黄—红基因表达、斜体基因名、两边坐标轴、底部横向颜色条，Helvetica；无原b号。输入是同次嵌入的细胞坐标及统一非负表达值，不进行MAGIC或拟时序估计。模拟Batf表达不代表实测；色条明确对应输入值。", "input": "同论文Fig.6b，连续蓝—浅黄—红基因表达、斜体基因名、两边坐标轴、底部横向颜色条，Helvetica；无原b号。输入是同次嵌入的细胞坐标及统一非负表达值，不进行MAGIC或拟时序估计。模拟Batf表达不代表实测；色条明确对应输入值。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + 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"同论文Fig.2c–d右侧图组。顶部七年红蓝方向组成与50%虚线，下部完整39基因响应气泡，共享列和右侧图例，Helvetica；当前图组独立呈现，不沿用c/d号。组成自主明确定义按每年原始P<.05基因的正/负数量归一，不作丰度加权；两类数量与完整273项结果保留，不将方向百分比解读为总体群落丰度或BH显著。", "input": "同论文Fig.2c–d右侧图组。顶部七年红蓝方向组成与50%虚线，下部完整39基因响应气泡，共享列和右侧图例，Helvetica；当前图组独立呈现，不沿用c/d号。组成自主明确定义按每年原始P<.05基因的正/负数量归一，不作丰度加权；两类数量与完整273项结果保留，不将方向百分比解读为总体群落丰度或BH显著。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, { "name": "openxlsx", "version": "4.2.8.1", "license": "MIT + file LICENSE" }, { "name": "jsonlite", "version": "2.0.0", 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"dd6c02eca0aa730f", "2ccf5abb441a9f1f" ], "conditions": "同论文Fig.2d。39基因×7年份气泡、五生物地球化学过程侧线、基因斜体、灰格、红蓝灰原始P与四级|ln(W/C)|尺寸，Helvetica；无源d号。每年四对照/四增温独立小区原始规范化信号；实际ln(meanW/meanC)及delta方法SE、正态近似95%CI/原始P。各年分别计算，跨年同小区不当独立n；完整273项BH保留，显示仍为原图原始P探索性编码，不冒称全族显著。", "input": "同论文Fig.2d。39基因×7年份气泡、五生物地球化学过程侧线、基因斜体、灰格、红蓝灰原始P与四级|ln(W/C)|尺寸，Helvetica；无源d号。每年四对照/四增温独立小区原始规范化信号；实际ln(meanW/meanC)及delta方法SE、正态近似95%CI/原始P。各年分别计算，跨年同小区不当独立n；完整273项BH保留，显示仍为原图原始P探索性编码，不冒称全族显著。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, 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"patchwork::wrap_plots", "systemfonts::system_fonts", "sysfonts::font_families", "sysfonts::font_add", "showtext::showtext_opts", "showtext::showtext_auto", "stats::var", "stats::qnorm", "stats::pnorm", "stats::p.adjust", "ggplot2::theme_classic", "ggplot2::element_blank", "ggplot2::element_rect", "ggplot2::element_line", "stats::setNames", "ggtext::element_markdown", "ggplot2::ggsave" ], "pinnedReferences": [ { "repository": "https://github.com/thomasp85/patchwork", "commit": "6b1d88ce1da1c5cae3818d984edf80dc0bb3de8c", "license": "NOASSERTION", "role": "已检索的原作者资料版本；不等同于已安装包版本" } ], "verification": { "passed": true, "identicalPixels": true, "tiffRgb": true, "tiffLzw": true, "dimensions": [ 3307, 4488 ], "codeSha256": "a639dd6fe579fe77521d767800e248a391d207986ba45d352fdfdcc4c8a98840", "executableSha256": "d11e09a034bd009fed313267f3e54546da845955a12ebd9bc0e0a6bdd701d4bc", "verifiedCodeSha256": "a639dd6fe579fe77521d767800e248a391d207986ba45d352fdfdcc4c8a98840", "commentOnlyUpdate": false, "warnings": [] } }, "nc2020-gsea-enrichment": { "id": "nc2020-gsea-enrichment", "sourceIds": [ "6db78d2d0c7f4c17", "bf751dde7ad7a861" ], "conditions": "Scharer等2020，DOI10.1038/s41467-020-17798-x，Fig.5d。绿色有符号ES曲线、零线、NES/P、黑色命中条码与蓝白红方向条，三个基因集垂直排列；无原d号。完整背景上按|score|加权p=1，固定种子1000次基因标签置换，以同号置换均值计算NES、同号尾部加一经验P；三基因集完整族BH保存在返回结果，图中P为原始经验P。原论文GSEA置换方法与本库输入流程分别声明，不能把BH写成GSEA软件FDR。360基因×3集合演示数据；替换完整背景，不仅输入显著成员。", "input": "Scharer等2020，DOI10.1038/s41467-020-17798-x，Fig.5d。绿色有符号ES曲线、零线、NES/P、黑色命中条码与蓝白红方向条，三个基因集垂直排列；无原d号。完整背景上按|score|加权p=1，固定种子1000次基因标签置换，以同号置换均值计算NES、同号尾部加一经验P；三基因集完整族BH保存在返回结果，图中P为原始经验P。原论文GSEA置换方法与本库输入流程分别声明，不能把BH写成GSEA软件FDR。360基因×3集合演示数据；替换完整背景，不仅输入显著成员。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { 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"nc2020-isotope-mineralization-with-inset": { "id": "nc2020-isotope-mineralization-with-inset", "sourceIds": [ "3ca29538e08a0d85" ], "conditions": "Chen等2020 DOI10.1038/s41467-020-16071-5，Fig.4：DOM同位素贡献百分比、矿化速率与原公开累计量三响应；速率内嵌day6以后的同源放大窗，绝不以速率简单累加替代实测累计量。完整公开三重复、实际Helvetica字形和最终PDF原生RGB配色；day6至17的灰色厌氧背景、实空圆与倒三角编码。作者Source Data名为SE的全部328完整单元实际为SD，本图按原始重复重算真实SEM并在图注声明；不抄原P、不冒称误差棒与原图长度完全相同。移除原小图号。", "input": "Chen等2020 DOI10.1038/s41467-020-16071-5，Fig.4：DOM同位素贡献百分比、矿化速率与原公开累计量三响应；速率内嵌day6以后的同源放大窗，绝不以速率简单累加替代实测累计量。完整公开三重复、实际Helvetica字形和最终PDF原生RGB配色；day6至17的灰色厌氧背景、实空圆与倒三角编码。作者Source Data名为SE的全部328完整单元实际为SD，本图按原始重复重算真实SEM并在图注声明；不抄原P、不冒称误差棒与原图长度完全相同。移除原小图号。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": 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C分母合计1000。土柱均值水平堆叠，两个来源分别共用尺度；24项质地Welch比较统一Holm，星号位于当前组分中心。原PDF残留Calibri白色不可见字，不作为可见图形标签；实际可见轴、标题、图例为Arial。", "input": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.2。独立模拟六土柱，每土柱三层×两个互斥碳来源×四组分完整输入；共同当前bulk C分母合计1000。土柱均值水平堆叠，两个来源分别共用尺度；24项质地Welch比较统一Holm，星号位于当前组分中心。原PDF残留Calibri白色不可见字，不作为可见图形标签；实际可见轴、标题、图例为Arial。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, { "name": "openxlsx", "version": "4.2.8.1", "license": "MIT + file LICENSE" }, { "name": "jsonlite", "version": "2.0.0", "license": "MIT + file LICENSE" }, { "name": "ggtext", "version": "0.1.2", "license": "GPL-2" }, { "name": "patchwork", "version": "1.3.2", "license": "MIT + file LICENSE" } ], "functions": [ "BiocManager::install", "readxl::read_excel", "utils::read.csv", "grDevices::pdf", "showtext::showtext_begin", "showtext::showtext_end", "grDevices::dev.off", "grid::grid.newpage", "patchwork::patchworkGrob", "ggplot2::ggplotGrob", "ggplot2::ggplot", "ggplot2::annotation_custom", "ggplot2::theme_void", "ggplot2::theme", "ggplot2::margin", "ggplot2::aes", "ggplot2::geom_col", "ggplot2::coord_flip", "ggplot2::scale_fill_manual", "ggplot2::scale_y_continuous", "ggplot2::labs", "ggtext::element_markdown", "ggplot2::geom_text", "patchwork::wrap_plots", "patchwork::plot_layout", "grDevices::pdfFonts", "stats::t.test", "stats::p.adjust", "ggplot2::theme_classic", "ggplot2::element_text", "ggplot2::element_line", "ggplot2::element_blank", "systemfonts::system_fonts", "sysfonts::font_families", "sysfonts::font_add", "showtext::showtext_opts", "showtext::showtext_auto", "stats::sd", "stats::setNames", "grid::unit", "ggplot2::ggsave" ], "pinnedReferences": [ { "repository": "https://github.com/thomasp85/patchwork", "commit": "6b1d88ce1da1c5cae3818d984edf80dc0bb3de8c", "license": "NOASSERTION", "role": "已检索的原作者资料版本；不等同于已安装包版本" } ], "verification": { "passed": true, "identicalPixels": true, "tiffRgb": true, "tiffLzw": true, "dimensions": [ 6259, 3425 ], "codeSha256": "3815f23a2aee949c191e0516083ee59bebc0be98839bd4bc19c6b35ffb6e64ef", "executableSha256": "607c5bcfaf6d1bb3f206075e6bea2ac6752ef5ce503a89d7ae329cdbd3588a73", "verifiedCodeSha256": "50f7afc414e1774756db1a065340b700a1f5e11399d674b1e82f3f47d880b87c", "commentOnlyUpdate": true, "warnings": [] } }, "nc2021-isotope-respiration-endpoint": { "id": "nc2021-isotope-respiration-endpoint", "sourceIds": [ "109be3b3d146243b" ], "conditions": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.1。独立模拟两质地×两处理×五土柱完整时间序列；面积图按土柱先计算再求均值。终点柱为均值±SD，激发为两个独立组均值差，差的离散量传播两组方差；质地激发比较使用四组差之差及Satterthwaite自由度，不强行配对。三终点Welch检验用Holm调整；没有原小图字母。", "input": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.1。独立模拟两质地×两处理×五土柱完整时间序列；面积图按土柱先计算再求均值。终点柱为均值±SD，激发为两个独立组均值差，差的离散量传播两组方差；质地激发比较使用四组差之差及Satterthwaite自由度，不强行配对。三终点Welch检验用Holm调整；没有原小图字母。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, { "name": "openxlsx", "version": "4.2.8.1", "license": "MIT + file LICENSE" }, { "name": "jsonlite", "version": "2.0.0", "license": "MIT + file LICENSE" }, { "name": "ggtext", "version": "0.1.2", "license": "GPL-2" }, { "name": "patchwork", "version": "1.3.2", "license": "MIT + file LICENSE" } ], "functions": [ "BiocManager::install", "readxl::read_excel", "utils::read.csv", "grDevices::pdf", "showtext::showtext_begin", "showtext::showtext_end", "grDevices::dev.off", "grid::grid.newpage", "patchwork::patchworkGrob", "ggplot2::ggplotGrob", "ggplot2::ggplot", "ggplot2::annotation_custom", "ggplot2::theme_void", "ggplot2::theme", "ggplot2::margin", "ggplot2::aes", "ggplot2::geom_area", "ggplot2::scale_fill_manual", "ggplot2::scale_x_continuous", "ggplot2::labs", "ggplot2::geom_col", "ggplot2::geom_errorbar", "ggplot2::expansion", "ggplot2::geom_segment", "ggplot2::geom_point", "ggplot2::position_jitter", "ggplot2::geom_text", "ggplot2::coord_cartesian", "ggplot2::element_text", "patchwork::wrap_plots", "patchwork::wrap_elements", "grDevices::pdfFonts", "grid::unit", "grid::rectGrob", "grid::gpar", "grid::segmentsGrob", "grid::grobTree", "grid::textGrob", "ggplot2::theme_classic", "ggtext::element_markdown", "ggplot2::element_line", "ggplot2::element_blank", "stats::sd", "stats::var", "stats::t.test", "stats::pt", "stats::p.adjust", "systemfonts::system_fonts", "sysfonts::font_families", "sysfonts::font_add", "showtext::showtext_opts", "showtext::showtext_auto", "stats::setNames", "ggplot2::ggsave" ], "pinnedReferences": [ { "repository": "https://github.com/thomasp85/patchwork", "commit": "6b1d88ce1da1c5cae3818d984edf80dc0bb3de8c", "license": "NOASSERTION", "role": "已检索的原作者资料版本；不等同于已安装包版本" } ], "verification": { "passed": true, "identicalPixels": true, "tiffRgb": true, "tiffLzw": true, "dimensions": [ 5669, 4370 ], "codeSha256": "be12c4836e581bc3b83a3deb15116bbaca4fc9e39c6dd17dc95fd05f84e36860", "executableSha256": "d73f5fe8ef0c61fc1f9a875bcf600009c7640948f2d68f99801d9c3d3b61a78d", "verifiedCodeSha256": "2e83af5fd1c6a9e151616ee9573a442e20f91f764d8f8a227ee31709298fc6ea", "commentOnlyUpdate": true, "warnings": [] } }, "nc2021-isotope-two-denominator-composite": { "id": "nc2021-isotope-two-denominator-composite", "sourceIds": [ "109be3b3d146243b" ], "conditions": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.5。四组为互斥模拟标志物集合；左图标记丰度在全部标记组间的分配百分比（每土柱土层合计100）；右图同一组的标记/(标记+未标记)，均值±SD及全部土柱点。12项同深度同组质地Welch比较统一Holm，四组间字母由土柱区组ANOVA和组内Tukey重算，不照抄来源原始星号或字母。双分母不是同一组成比例改名。", "input": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.5。四组为互斥模拟标志物集合；左图标记丰度在全部标记组间的分配百分比（每土柱土层合计100）；右图同一组的标记/(标记+未标记)，均值±SD及全部土柱点。12项同深度同组质地Welch比较统一Holm，四组间字母由土柱区组ANOVA和组内Tukey重算，不照抄来源原始星号或字母。双分母不是同一组成比例改名。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, { "name": "openxlsx", "version": "4.2.8.1", "license": "MIT + file LICENSE" }, { "name": "jsonlite", "version": "2.0.0", "license": "MIT + file LICENSE" }, { "name": "ggtext", "version": "0.1.2", "license": "GPL-2" }, { "name": "patchwork", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "multcompView", "version": "0.1.12", "license": "GPL-2" } ], "functions": [ "BiocManager::install", "readxl::read_excel", "utils::read.csv", "grDevices::pdf", "showtext::showtext_begin", "showtext::showtext_end", "grDevices::dev.off", "grid::grid.newpage", "patchwork::patchworkGrob", "ggplot2::ggplotGrob", "ggplot2::ggplot", "ggplot2::annotation_custom", "ggplot2::theme_void", "ggplot2::theme", "ggplot2::margin", "ggplot2::aes", "ggplot2::geom_col", "ggplot2::scale_fill_manual", "ggplot2::scale_y_continuous", "ggplot2::scale_x_continuous", "ggplot2::expansion", "ggplot2::coord_cartesian", "ggplot2::annotate", "ggplot2::labs", "ggplot2::geom_errorbar", "ggplot2::geom_point", "ggplot2::position_jitter", "ggplot2::geom_text", "patchwork::wrap_plots", "grDevices::pdfFonts", "stats::aov", "stats::TukeyHSD", "multcompView::multcompLetters", "stats::t.test", "stats::p.adjust", "ggplot2::theme_classic", "ggplot2::element_text", "ggtext::element_markdown", "ggplot2::element_line", "ggplot2::element_blank", "systemfonts::system_fonts", "sysfonts::font_families", "sysfonts::font_add", "showtext::showtext_opts", "showtext::showtext_auto", "stats::sd", "stats::setNames", "grid::unit", "ggplot2::ggsave" ], "pinnedReferences": [ { "repository": "https://github.com/thomasp85/patchwork", "commit": "6b1d88ce1da1c5cae3818d984edf80dc0bb3de8c", "license": "NOASSERTION", "role": "已检索的原作者资料版本；不等同于已安装包版本" } ], "verification": { "passed": true, "identicalPixels": true, "tiffRgb": true, "tiffLzw": true, "dimensions": [ 6732, 3425 ], "codeSha256": "9e612ee535ff6b840934bfbd84f11ea5106f8639f5e6a9144fad05c7aaf6a1ef", "executableSha256": "d3cb0cd0cbdbbb5a5bfb8a57495c504c6ad9e914a5ec6a24865738828a467d17", "verifiedCodeSha256": "1082106368140b6281b90b11666c8a29412563904bb5d297062c929e7a74e825", "commentOnlyUpdate": true, "warnings": [] } }, "nc2021-nmr-region-stacked-spectra": { "id": "nc2021-nmr-region-stacked-spectra", "sourceIds": [ "109be3b3d146243b" ], "conditions": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.3。完整模拟641点谱网格和真实独立测量ID；每谱用梯形积分归一后平均，全部曲线用同一缩放常数并分别垂直平移。两质地、三组分彩色凋落物谱与黑色虚线对照叠加；ppm下降、五分界与四化学区标签。无原峰位或化学结论声称，无P值。", "input": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.3。完整模拟641点谱网格和真实独立测量ID；每谱用梯形积分归一后平均，全部曲线用同一缩放常数并分别垂直平移。两质地、三组分彩色凋落物谱与黑色虚线对照叠加；ppm下降、五分界与四化学区标签。无原峰位或化学结论声称，无P值。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, { "name": "openxlsx", "version": "4.2.8.1", "license": "MIT + file LICENSE" }, { "name": "jsonlite", "version": "2.0.0", "license": "MIT + file LICENSE" }, { "name": "ggtext", "version": "0.1.2", "license": "GPL-2" }, { "name": "patchwork", "version": "1.3.2", "license": "MIT + file LICENSE" } ], "functions": [ "BiocManager::install", "jsonlite::base64_dec", "readxl::read_excel", "utils::read.csv", "grDevices::pdf", "showtext::showtext_begin", "showtext::showtext_end", "grDevices::dev.off", "grid::grid.newpage", "patchwork::patchworkGrob", "ggplot2::ggplotGrob", "ggplot2::ggplot", "ggplot2::annotation_custom", "ggplot2::theme_void", "ggplot2::theme", "ggplot2::margin", "ggplot2::aes", "ggplot2::geom_vline", "ggplot2::geom_line", "ggplot2::geom_text", "ggplot2::facet_wrap", "ggplot2::scale_color_manual", "ggplot2::scale_linetype_manual", "ggplot2::scale_x_reverse", "ggplot2::coord_cartesian", "ggplot2::labs", "ggplot2::element_blank", "ggplot2::element_text", "grid::unit", "ggplot2::guides", "ggplot2::guide_legend", "grDevices::pdfFonts", "stats::aggregate", "ggplot2::theme_classic", "ggtext::element_markdown", "ggplot2::element_line", "ggplot2::draw_key_rect", "ggplot2::draw_key_path", "systemfonts::system_fonts", "sysfonts::font_families", "sysfonts::font_add", "showtext::showtext_opts", "showtext::showtext_auto", "stats::setNames", "ggplot2::ggsave" ], "pinnedReferences": [ { "repository": "https://github.com/thomasp85/patchwork", "commit": "6b1d88ce1da1c5cae3818d984edf80dc0bb3de8c", "license": "NOASSERTION", "role": "已检索的原作者资料版本；不等同于已安装包版本" } ], "verification": { "passed": true, "identicalPixels": true, "tiffRgb": true, "tiffLzw": true, "dimensions": [ 4724, 4488 ], "codeSha256": "eda1212690eff5636ba15721f78248c58b97408371ba77e976c86046b30b42ac", "executableSha256": "d8fe18974e18cc619f70f23d7642ead46a2b126484049aba7414aaf00aff435e", "verifiedCodeSha256": "fe828364af2af3c9129e3db2b89259808910c3e02d2e3193bf2bb983aeb33336", "commentOnlyUpdate": true, "warnings": [] } }, "nc2021-plfa-hatched-repeated-depth": { "id": "nc2021-plfa-hatched-repeated-depth", "sourceIds": [ "109be3b3d146243b" ], "conditions": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.4。模拟完整两质地、两处理、三个独立土柱及三层×四标志物；左右总量与组分组合，白色斜纹表示对照，原始土柱点、均值±SD和实际统计。总Bacteria包含Gram±，总PLFA只加Bacteria与Fungi。三层比较采用土柱区组ANOVA与Tukey调整而不是把三层当独立重复；30项独立处理比较统一Holm。原图使用Calibri的局部文字须核对，不据Arial主体字体假装全部一致。", "input": "Witzgall等2021 DOI10.1038/s41467-021-24192-8，Fig.4。模拟完整两质地、两处理、三个独立土柱及三层×四标志物；左右总量与组分组合，白色斜纹表示对照，原始土柱点、均值±SD和实际统计。总Bacteria包含Gram±，总PLFA只加Bacteria与Fungi。三层比较采用土柱区组ANOVA与Tukey调整而不是把三层当独立重复；30项独立处理比较统一Holm。原图使用Calibri的局部文字须核对，不据Arial主体字体假装全部一致。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, { "name": "openxlsx", "version": "4.2.8.1", "license": "MIT + file LICENSE" }, { "name": "jsonlite", "version": "2.0.0", "license": "MIT + file LICENSE" }, { "name": "ggtext", "version": "0.1.2", "license": "GPL-2" }, { "name": 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Fig.2A。40疾病性状分块、四类型符号、八类别颜色、基因斜体标注、2.5e−6红点参考线和10.2–14.8空白断轴，Arial；无源A号。16000项明确模拟的完整上游基因检验结果；先对全部输入一族BH，再按原图P≤.01显示窗口。纵轴是原始−log10(P)，红线仅原图固定参考，不能冒称通用FDR阈值；不在此拟合SKAT。断轴内存在点即拒绝绘图，所有结果与q保留。源填色为JPEG，使用发表色块内部RGB中位数，不能声称无损原矢量色值。", "input": "Yang等2024 DOI10.1038/s41467-024-49782-0 Fig.2A。40疾病性状分块、四类型符号、八类别颜色、基因斜体标注、2.5e−6红点参考线和10.2–14.8空白断轴，Arial；无源A号。16000项明确模拟的完整上游基因检验结果；先对全部输入一族BH，再按原图P≤.01显示窗口。纵轴是原始−log10(P)，红线仅原图固定参考，不能冒称通用FDR阈值；不在此拟合SKAT。断轴内存在点即拒绝绘图，所有结果与q保留。源填色为JPEG，使用发表色块内部RGB中位数，不能声称无损原矢量色值。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": 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"id": "nc2024-mutation-expression-density", "sourceIds": [ "83c926ed89fe822d" ], "conditions": "Yang等2024 DOI10.1038/s41467-024-49782-0，最终发表 Fig.5A。16蛋白四列密度分面、携带者黄/非携带者蓝填充、黑色轮廓、真实中位数垂线和完整q值，Arial，无源A号。1920个明确模拟受试者×蛋白观察，各蛋白共享40携带者/80非携带者；实际双侧Welch t、完整16族BH和nrd0 KDE，明示独立统计实现。输入须为上游规范化值，没有按看到的显著性删蛋白或在此静默截去五SD外观测。", "input": "Yang等2024 DOI10.1038/s41467-024-49782-0，最终发表 Fig.5A。16蛋白四列密度分面、携带者黄/非携带者蓝填充、黑色轮廓、真实中位数垂线和完整q值，Arial，无源A号。1920个明确模拟受试者×蛋白观察，各蛋白共享40携带者/80非携带者；实际双侧Welch t、完整16族BH和nrd0 KDE，明示独立统计实现。输入须为上游规范化值，没有按看到的显著性删蛋白或在此静默截去五SD外观测。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License 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"showtext::showtext_opts", "showtext::showtext_auto", "stats::setNames", "ggtext::element_markdown", "ggplot2::theme_void", "ggplot2::ggsave" ], "pinnedReferences": [], "verification": { "passed": true, "identicalPixels": true, "tiffRgb": true, "tiffLzw": true, "dimensions": [ 4724, 4370 ], "codeSha256": "28a236af6753054947c45be9cf9fae6525a5d25373e8f9c08985f969bd329394", "executableSha256": "53f4c9392b469e88960815e7fada9537b74d6d9d71ddce0d6c5408e2ee349e52", "verifiedCodeSha256": "28a236af6753054947c45be9cf9fae6525a5d25373e8f9c08985f969bd329394", "commentOnlyUpdate": false, "warnings": [] } }, "nc2024-or-median-iqr": { "id": "nc2024-or-median-iqr", "sourceIds": [ "83c926ed89fe822d" ], "conditions": "同论文Fig.2D。五类OR的Q1–Q3矩形、真实中位数横线、前两类白色中线、后三级黑色、无箱须/离群点，右侧蓝色类别图例，Arial；无源D号。301项模拟关联使用type=7分位数；箱体是数据IQR，不是均值95%CI或标准Tukey箱线图。不显示不存在的显著性检验。", "input": "同论文Fig.2D。五类OR的Q1–Q3矩形、真实中位数横线、前两类白色中线、后三级黑色、无箱须/离群点，右侧蓝色类别图例，Arial；无源D号。301项模拟关联使用type=7分位数；箱体是数据IQR，不是均值95%CI或标准Tukey箱线图。不显示不存在的显著性检验。", 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DOI10.1038/s41467-024-49782-0，最终发表 Fig.6A。同基因多表型OR点、四检验符号、五表型类别颜色、95%Wald区间和OR=1线，Arial，无源A号。完整60个模拟上游logOR与SE；全族双侧Wald/BH后展示q<.05，区间由exp(beta±1.96SE)实际重算。完整背景未以显著子集重新校正，参考线不是效果方向的统计证据。", "input": "Yang等2024 DOI10.1038/s41467-024-49782-0，最终发表 Fig.6A。同基因多表型OR点、四检验符号、五表型类别颜色、95%Wald区间和OR=1线，Arial，无源A号。完整60个模拟上游logOR与SE；全族双侧Wald/BH后展示q<.05，区间由exp(beta±1.96SE)实际重算。完整背景未以显著子集重新校正，参考线不是效果方向的统计证据。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", "version": "0.9.8", "license": "Apache License (>= 2.0)" }, { "name": "readxl", "version": "1.4.5", "license": "MIT + file LICENSE" }, { "name": "openxlsx", "version": "4.2.8.1", "license": "MIT + 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"dimensions": [ 4724, 2125 ], "codeSha256": "92fc2e2e14e73d81aff2f2b7c623caac434da4212ebb5e7a70e3b6c8274579aa", "executableSha256": "51aa70732527f8f99e8c07269b440ea2c0efd156203cf50cf496d9ec95bd1666", "verifiedCodeSha256": "92fc2e2e14e73d81aff2f2b7c623caac434da4212ebb5e7a70e3b6c8274579aa", "commentOnlyUpdate": false, "warnings": [] } }, "nc2024-phenotype-beta-convergence": { "id": "nc2024-phenotype-beta-convergence", "sourceIds": [ "83c926ed89fe822d" ], "conditions": "Yang等2024 DOI10.1038/s41467-024-49782-0，最终发表 Fig.3B。疾病分块交替灰底、正负beta汇聚、gene颜色、exp(abs(beta))圆点、斜体基因名与零参考线，Arial，无源B号。144项完整模拟上游模型结果；原始P<5e-8仅展示筛选，完整BH结果留在analysis，不拟合GWAS，也不把零线称为显著性阈值。", "input": "Yang等2024 DOI10.1038/s41467-024-49782-0，最终发表 Fig.3B。疾病分块交替灰底、正负beta汇聚、gene颜色、exp(abs(beta))圆点、斜体基因名与零参考线，Arial，无源B号。144项完整模拟上游模型结果；原始P<5e-8仅展示筛选，完整BH结果留在analysis，不拟合GWAS，也不把零线称为显著性阈值。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": 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"commentOnlyUpdate": false, "warnings": [] } }, "nc2024-protein-domain-mutation-tracks": { "id": "nc2024-protein-domain-mutation-tracks", "sourceIds": [ "83c926ed89fe822d" ], "conditions": "Yang等2024 DOI10.1038/s41467-024-49782-0，最终发表 Fig.5C。四蛋白双列结构域轨道、实际氨基酸长度比例、上下分布变异红点/短线、物理间距避让与真实位点引线、旋转p.标签和结构域颜色，Arial，无源C号。明确模拟参考蛋白注释与48变异，不是Pfam查询或致病性预测；所有变异/域边界≤所给序列长度，同基因一个参考转录本，原图未给P因此不造检验。", "input": "Yang等2024 DOI10.1038/s41467-024-49782-0，最终发表 Fig.5C。四蛋白双列结构域轨道、实际氨基酸长度比例、上下分布变异红点/短线、物理间距避让与真实位点引线、旋转p.标签和结构域颜色，Arial，无源C号。明确模拟参考蛋白注释与48变异，不是Pfam查询或致病性预测；所有变异/域边界≤所给序列长度，同基因一个参考转录本，原图未给P因此不造检验。", "dependencies": [ { "name": "ggplot2", "version": "3.5.2", "license": "MIT + file LICENSE" }, { "name": "ragg", "version": "1.3.2", "license": "MIT + file LICENSE" }, { "name": "scales", "version": "1.4.0", "license": "MIT + file LICENSE" }, { "name": "systemfonts", "version": "1.2.3", "license": "MIT + file LICENSE" }, { "name": "sysfonts", "version": "0.8.9", "license": "GPL-2" }, { "name": "showtext", 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