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docs(tutorials): integrate FigureYa optimization references batch 17 (items 81-85, checklist order) - #456
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ShixiangWang wants to merge 9 commits into
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docs(tutorials): integrate FigureYa optimization references batch 17 (items 81-85, checklist order)#456ShixiangWang wants to merge 9 commits into
ShixiangWang wants to merge 9 commits into
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…(items 81-85, checklist order) Batch 17 (EN + zh, all rendered and visually gated): - FigureYa284pairwiseLogrank -> Clinics/KaplanMeierPlot: pairwise log-rank section (5-stratum KM + risk table + Holm-adjusted pairwise_survdiff matrix via ggpp) - FigureYa28color -> Colors: k-means palette extraction from a reference figure (png + stats only), colorRampPalette interpolation, CVD simulation check - FigureYa290BarGraph -> Ranking/BarPlot sec 9: cell-type proportion bars with overall Fisher (Monte-Carlo) and rstatix row-wise BH post-hoc stars - FigureYa297Rbar -> Ranking/BarPlot sec 10: radial and horizontal gradient bars via ggpattern - FigureYa298ecdfPvalue -> Distribution/ECDFPlot sec 5: multi-group ECDF with two-sided Wilcoxon annotations vs reference Reliability audit of merged batches 1-16 (PRs #439-#455, items 1-80): independent review found 0 P0 scientific errors; this commit fixes all findings - 10 P1 (mis-numbered/dangling FigureYa citations in Heatmap, ComplexHeatmap, NetworkPlot, KaplanMeier, PieChart, Scatter, BlandAltman; claim-vs-code mismatches in ImmuneSubtypePlot, PCAplot, TumorIndexPlot; VennPlot exact-test overstatement retitled to binomial approximation) and 29 P2 (non-existent API names corrected, lost/duplicated headings restored, captions aligned with code, CellChat label geometry, KEGG demo de-duplication, Chord circle overlap, pheatmap phantom arg + double print, VennDiagram logs removed and logging disabled). All touched pages re-rendered locally; sync-gallery --check passes.
…(items 86-90, checklist order) - FigureYa2ggtree+pheatmap+msa -> Omics/MultiSeqsAlignment sec 4 (EN+zh): expression heatmap -> MSA -> NJ tree loop on a simulated no-indel gene family (pheatmap + ggmsa + ape::nj + ggtree; msa/seqinr route noted) - FigureYa30nomogram_update -> Clinics/Nomogram sec 3 (EN+zh): rms::cph + calibrate() bootstrap calibration at 3 and 5 years on TCGA-LIHC - FigureYa30Plus_nomogram_app -> Clinics/Nomogram: interactive web app note - FigureYa310CPDBChordGramV2 -> Omics/CellChatCirclePlot sec 7 (EN+zh): two-group differential communication as a hierarchical edge-bundled chord (ggraph dendrogram + geom_conn_bundle; tree-only graph, bundle logFC via con.id) - FigureYa311PAM50Heatmap -> Correlation/Heatmap sec 4.10 (EN+zh): subtype-centroid heatmap with signature-score top annotations (nearest-centroid SSP stand-in, gene-set-mean scores)
…(items 91-95, checklist order) - FigureYa313CircularPlot -> Proportion/ChordDiagram sec 5 (EN+zh): two-ring score comparison with an index-patient pointer (circlize spare-sector trick) - FigureYa318GenesetDEDotplot -> Omics/TextEnrichmentBarPlot sec 4 (EN+zh): pathway-activity DE dot plot across cell types with classification strip - FigureYa321volcanoSE -> Omics/VolcanoPlot sec 4 (EN+zh): size-encoded volcano for small-effect PDUI screens (limma pipeline as in the reference) - FigureYa33DCA_update -> Clinics/DCAPlot sec 5 (EN+zh): four-model survival decision curves + net interventions avoided incl. a deliberately weak model - FigureYa35batch_bestSeparationV3_update -> Clinics/KaplanMeierPlot (EN+zh): batch optimal cutpoints via surv_cutpoint with HR/CI table and KM grid; multiple-testing caveat made explicit
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✅ QMD Format Check✅ All 37 checked QMD file(s) pass format validation!
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📊 Quarto Render PreviewThe new or modified Quarto files have been rendered and are available as artifacts. 🔗 View and Download Rendered Files Click the link above, scroll to the "Artifacts" section at the bottom of the page, and download Modified files: |
…(items 96-100, checklist order) - FigureYa37correlationV2_update -> Correlation/Correlogram sec 6 (EN+zh): correlation chord with width-encoded |cor| links and signed colour ramp (circlize, sub-segment slicing kept from the reference) - FigureYa38PCA -> Correlation/PCAplot sec 9 (EN+zh): top-N loading arrows (loading x sqrt(eigenvalue)) with nested 90/95% confidence ellipses (dependency-free ggplot2, ggord route noted) - FigureYa39bar -> Ranking/BarPlot sec 11 (EN+zh): NEJM-style per-type coloured waterfall with RECIST reference lines and clipped axis, plus the diverging GSVA-style gray/colored bar layout - FigureYa3genomeView -> Omics/ChromosomePlot sec 12 (EN+zh): IGV-style signal tracks around a gene locus without Gviz (per-kb bins + dedicated gene-model facet track) - FigureYa42oncoprintV2_update -> Omics/MutationOncoplot sec 11 (EN+zh): 01-matrix oncoprint with pathway row_split and clinical bottom annotation
…(items 101-105, checklist order) - FigureYa43ManhattanV2 -> Omics/ManhattanPlot sec 3 (EN+zh): ggplot2 Manhattan with repelled gene+rsID labels, threshold-sized points, alternating colours - FigureYa44profile -> Ranking/Parallel sec 3 (EN+zh): metagene profile over compressed gene bodies, IP vs Input (rtracklayer route noted) - FigureYa47HRtable -> Clinics/RegressionTable sec 7 (EN+zh): grouped HR table with batch univariate -> multivariate Cox on training + validation cohorts - FigureYa4bestSeparation -> Clinics/KaplanMeierPlot (EN+zh): optimal-split landscape (-log10P vs log2HR at every dichotomisation) + median/best KM pair - FigureYa52GOplot -> Omics/TextEnrichmentBarPlot sec 5 (EN+zh): gene-concept network via clusterProfiler::enrichGO + simplify + enrichplot::cnetplot (GOplot itself no longer on CRAN)
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✅ QMD Format Check✅ All 41 checked QMD file(s) pass format validation!
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…(items 106-110, checklist order) - FigureYa55panCancer_violinV2 -> Distribution/ViolinPlot sec 5 (EN+zh): pan-cancer split violin via ggdist::stat_halfeye(side=) with quartile dashes and per-tissue Wilcoxon stars (GeomSplitViolin route retired) - FigureYa55plus_pancancer_boxplot -> Distribution/BoxPlot sec 4 (EN+zh): ggpubr pan-cancer boxplot with jitter and manual per-tissue stars - FigureYa57profile_1bw -> Ranking/Parallel sec 4 (EN+zh): single-sample profile across region classes (HCP/ICP/LCP promoter metagene) - FigureYa59Plus_volcano_shiny -> Omics/iVolcanoPlot sec 4 (EN+zh): Shiny app note (run locally, inputs mirror the static tiered volcano) - FigureYa59volcanoV2 -> Omics/VolcanoPlot sec 5 (EN+zh): tiered volcano with nested gates, pathway-coloured validation picks
…ssing the package)
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✅ QMD Format Check✅ All 42 checked QMD file(s) pass format validation!
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… has no default repos)
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✅ QMD Format Check✅ All 42 checked QMD file(s) pass format validation!
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Contributor
📊 Quarto Render PreviewThe new or modified Quarto files have been rendered and are available as artifacts. 🔗 View and Download Rendered Files Click the link above, scroll to the "Artifacts" section at the bottom of the page, and download Modified files: |
…(items 111-115, checklist order) - FigureYa5bubbles -> Correlation/Bubble sec 3 (EN+zh): motif P-value size x TF expression fill bubble grid with reference-style clamps - FigureYa60GSEA_clusterProfilerV2 -> Omics/GseaPlot sec 9 (EN+zh): clusterProfiler::GSEA with TERM2GENE built from the orgDb GO mapping and enrichplot::gseaplot2 three-panel output (4.x API notes included) - FigureYa62twoAxis -> DataOverTime/LineChart sec 13 (EN+zh): double-Y-axis scatter with pre-scaled secondary series, coord_fixed ratio and per-series Pearson annotations - FigureYa64triangle -> Correlation/TernaryPlot sec 4 (EN+zh): ternary mutation-frequency composition with the reference's segmented size scaling - FigureYa66UnivariateCox -> Clinics/RegressionTable sec 8 (EN+zh): batch univariate Cox forest plot with HR CI diamonds on log2 x, viridis p colour
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✅ QMD Format Check✅ All 45 checked QMD file(s) pass format validation!
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📊 Quarto Render PreviewThe new or modified Quarto files have been rendered and are available as artifacts. 🔗 View and Download Rendered Files Click the link above, scroll to the "Artifacts" section at the bottom of the page, and download Modified files: |
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FigureYa integration — batch 17 + full reliability audit of batches 1–16
Closes part of #436. Same PR will receive subsequent batches (5 items each) until the checklist is complete, per the integration plan.
Batch 17 (items 81–85, checklist order, EN + zh)
Clinics/KaplanMeierPlot.qmd— new §Pairwise log-rank comparisons across many groups: 5-stratum KM + risk table + overall log-rank p + Holm-adjustedpairwise_survdiff()matrix embedded withggpp::geom_table()Colors.qmd— new Part III section "borrowing a palette from a figure you admire":png::readPNG()+ achromatic-pixel filtering +kmeans()extraction,colorRampPalette()interpolation, CVD-simulation checkRanking/BarPlot.qmd§9 — cell-type proportion bars + overall Fisher (Monte-Carlo) +rstatix::row_wise_fisher_test()BH post-hoc with stars; replicate facet uses the same cellsRanking/BarPlot.qmd§10 — radial and horizontal (mirrored halves) gradient bars viaggpattern::geom_col_pattern()Distribution/ECDFPlot.qmd§5 — three-group ECDF annotated with two-sided Wilcoxon rank-sum p vs reference (colored,p < 0.001guarded); Kruskal–Wallis equivalence noted and verifiedAll 10 new figures rendered, passed the visual gate (5 after one repair round: in-figure table label, legend occlusion, same-cells consistency across facets, white-label contrast on gradients, canvas letterboxing).
Reliability audit of already-merged batches (#439–#455, items 1–80)
Two independent review passes over all 14 merged PRs, including execution of the seeded statistical code and FigureYa original cross-checks. Result: 0 P0 scientific errors. Found and fixed in this PR:
[4], NetworkPlot dangling[9]/[10], KM/PieChart/Scatter/BlandAltman gaps), plus 3 claim-vs-code mismatches rewritten honestly (ImmuneSubtype "opposite module" → independent latent factors; PCA 3D "PC2 colour-coding" caption; TumorIndex cohort split now interleaves so both cohorts span all four stages) and the VennPlot §6 "exact multiset-intersection test" retitled to what it computes — a slightly conservative binomial approximation (SuperExactTestMSET()documented as the exact method).ConsensusClusterPlus(),pfamDomains(),fgseaMultilevel(),compareCluster(),trinucleotideMatrix(),layout_in_circle,aplot::annotation_boxplot()→ggsignif::geom_signif()), 5 lost/duplicated headings restored, z-score direction / channel-count / window-size captions aligned with code, CellChat circle labels moved onto their nodes, KEGG demo de-duplicated (hsa04115 = p53 signaling, official "Organismal Systems"), Chord diagram circles separated,pheatmapphantomname=+ double print fixed, 12 strayVennDiagram.*.logfiles removed anddisable.logging = TRUEadded to allvenn.diagram()calls.Every code-touching page re-rendered locally (all green) and
sync-gallery --checkpasses.