@openbiox/bizard-mcp 0.1.3 → 0.2.0

package/dist/snapshot/llms.txt

@@ -1,7 +1,7 @@
 # Bizard
 
 > An open atlas of biomedical data visualization tutorials (R/Python/Julia).
-> License: CC-BY-NC-4.0. Paper: https://arxiv.org/abs/2503.06845
+> License: CC-BY-NC-4.0. Paper: https://doi.org/10.1002/imm3.70038
 
 ## Animation (动画)
 - [Scattered Bubble Animation](https://openbiox.github.io/Bizard/Animation/Animation.html#taking-the-gapminder-dataset-as-an-example)
@@ -126,6 +126,7 @@
 - [Waterfalls Plot2](https://openbiox.github.io/Bizard/Hiplot/185-waterfalls-plot.html)
 - [Waterfalls](https://openbiox.github.io/Bizard/Hiplot/186-waterfalls.html)
 - [PCA](https://openbiox.github.io/Bizard/Hiplot/187-pca.html)
+- [Basic radial stacked bar plot](https://openbiox.github.io/Bizard/Composition/RadialStackedBar.html#fig-1.1BasicRadialStacked)
 
 ## CLINICS
 - [Barplot](https://openbiox.github.io/Bizard/Hiplot/010-barplot.html)
@@ -179,6 +180,11 @@
 - [Collinearity Plot](https://openbiox.github.io/Bizard/Omics/CollinearityPlot.html#basic-collinearity-plot)
 - [Collinearity Plot](https://openbiox.github.io/Bizard/Omics/CollinearityPlot.html#change-colors)
 
+## CombinationPanel
+- [Bar, beeswarm and paired line panels of the sleep study](https://openbiox.github.io/Bizard/Clinics/CombinationPanel.html#fig-1.1ComboPanels)
+- [Stacked combination panel with a paired t-test annotation](https://openbiox.github.io/Bizard/Clinics/CombinationPanel.html#fig-1.2StackedCombo)
+- [Paired slopes with the mean trajectory highlighted](https://openbiox.github.io/Bizard/Clinics/CombinationPanel.html#fig-1.3MeanTrajectory)
+
 ## Composition (组成)
 - [Barplot Using iris Data](https://openbiox.github.io/Bizard/Composition/GroupedBarplot.html#grouped-bar-chart)
 - [Barplot Using iris Data](https://openbiox.github.io/Bizard/Composition/GroupedBarplot.html#stacked-bar-chart)
@@ -246,6 +252,11 @@
 - [Basic Waffle Chart Using ggplot2 Package](https://openbiox.github.io/Bizard/Composition/Waffle.html#taking-the-mtcars-database-as-an-example-1)
 - [Basic Waffle Chart Using ggplot2 Package](https://openbiox.github.io/Bizard/Composition/Waffle.html#grouping)
 - [Basic Waffle Chart Using ggplot2 Package](https://openbiox.github.io/Bizard/Composition/Waffle.html#grouping)
+- [Basic circular multi-track sample annotation plot](https://openbiox.github.io/Bizard/Composition/CircularAnnotation.html#fig-1.1BasicCircular)
+- [Circular annotation plot with summary panels in the gap](https://openbiox.github.io/Bizard/Composition/CircularAnnotation.html#fig-1.2FullCircular)
+- [Customized annotation plot: sorted by BMI with a 120-degree gap](https://openbiox.github.io/Bizard/Composition/CircularAnnotation.html#fig-1.3CustomCircular)
+- [Species proportions per island with a donut hole](https://openbiox.github.io/Bizard/Composition/RadialStackedBar.html#fig-1.2ProportionRadialStacked)
+- [Sectors sorted by the Gentoo share](https://openbiox.github.io/Bizard/Composition/RadialStackedBar.html#fig-1.3SortedRadialStacked)
 
 ## Correlation (相关)
 - [Basic Scatter Plot](https://openbiox.github.io/Bizard/Correlation/Scatter.html#fig-BasicPlot)
@@ -366,6 +377,9 @@
 - [Theme Change for Ternary Plot](https://openbiox.github.io/Bizard/Correlation/TernaryPlot.html#fig-Fig3)
 - [Beautify Ternary Plot](https://openbiox.github.io/Bizard/Correlation/TernaryPlot.html#fig-Fig4)
 - [RColorBrewer Basic R](https://openbiox.github.io/Bizard/Correlation/Heatmap.html#fig-RColorBrewerBasicR)
+- [Basic bubble heatmap of the top PBMC markers](https://openbiox.github.io/Bizard/Correlation/BubbleHeatmap.html#fig-1.1BasicBubbleHeatmap)
+- [Refined bubble heatmap with gene-block separators](https://openbiox.github.io/Bizard/Correlation/BubbleHeatmap.html#fig-1.2RefinedBubbleHeatmap)
+- [Bubble heatmap coloured by significance](https://openbiox.github.io/Bizard/Correlation/BubbleHeatmap.html#fig-1.3SignificanceBubbleHeatmap)
 
 ## Distribution (分布)
 - [Basic Violin Plot](https://openbiox.github.io/Bizard/Distribution/ViolinPlot.html#fig-1.1BasicViolin)
@@ -450,6 +464,9 @@
 - [More Advanced Radial Column Chart](https://openbiox.github.io/Bizard/Distribution/RadialColumnChart.html#fig-2.2DensityCurve)
 - [Histogram mean or median distribution distance](https://openbiox.github.io/Bizard/Distribution/Histogram.html#fig-OverlappingHistogramsMean)
 - [Basic violin plot with significance annotation of differences between groups](https://openbiox.github.io/Bizard/Distribution/ViolinPlot.html#fig-1.4BasicViolinSignificance)
+- [Basic raincloud plot of penguin body mass](https://openbiox.github.io/Bizard/Distribution/RaincloudPlot.html#fig-1.1BasicRaincloud)
+- [Raincloud plot with mean markers and sample sizes](https://openbiox.github.io/Bizard/Distribution/RaincloudPlot.html#fig-1.2AnnotatedRaincloud)
+- [Horizontal raincloud plot](https://openbiox.github.io/Bizard/Distribution/RaincloudPlot.html#fig-1.3HorizontalRaincloud)
 
 ## Evolution
 - [Basic Line Chart](https://openbiox.github.io/Bizard/DataOverTime/LineChart.html#fig-BasicPlot)
@@ -514,6 +531,11 @@
 - [English Calendar](https://openbiox.github.io/Bizard/DataOverTime/CalendHighlight.html#english-calendar)
 - [Calendar Period](https://openbiox.github.io/Bizard/DataOverTime/CalendHighlight.html#calendar-period)
 
+## FcFcPlot
+- [Basic FC-FC Scatter Plot](https://openbiox.github.io/Bizard/Omics/FcFcPlot.html#fig-1.1BasicFcFc)
+- [Color points by significance category](https://openbiox.github.io/Bizard/Omics/FcFcPlot.html#fig-1.2CategoryFcFc)
+- [FC-FC scatter plot with significance-scaled points and curated gene labels](https://openbiox.github.io/Bizard/Omics/FcFcPlot.html#fig-1.3LabelFcFc)
+
 ## GeneStructurePlot
 - [Gene Structure Plot](https://openbiox.github.io/Bizard/Omics/GeneStructurePlot.html#fig-1.1BasicPlot)
 - [Gene Structure Plot](https://openbiox.github.io/Bizard/Omics/GeneStructurePlot.html#fig-1.2GeneGroup)
@@ -538,6 +560,23 @@
 - [Scatter Plot (Julia)](https://openbiox.github.io/Bizard/Julia/ScatterPlot.html)
 - [Violin Plot (Julia)](https://openbiox.github.io/Bizard/Julia/ViolinPlot.html)
 - [Heatmap (Julia)](https://openbiox.github.io/Bizard/Julia/Heatmap.html)
+- [Bar Plot (Julia)](https://openbiox.github.io/Bizard/Julia/BarPlot.html)
+- [Box Plot (Julia)](https://openbiox.github.io/Bizard/Julia/BoxPlot.html)
+- [Histogram & Density Plot (Julia)](https://openbiox.github.io/Bizard/Julia/HistKdePlot.html)
+- [Line Plot (Julia)](https://openbiox.github.io/Bizard/Julia/LinePlot.html)
+- [Raincloud Plot (Julia)](https://openbiox.github.io/Bizard/Julia/RaincloudPlot.html)
+- [Pie & Donut (Julia)](https://openbiox.github.io/Bizard/Julia/PieDonutPlot.html)
+- [Area & Streamgraph (Julia)](https://openbiox.github.io/Bizard/Julia/AreaPlot.html)
+- [Lollipop & Dumbbell (Julia)](https://openbiox.github.io/Bizard/Julia/LollipopPlot.html)
+- [Correlogram (Julia)](https://openbiox.github.io/Bizard/Julia/CorrelogramPlot.html)
+- [Radar Plot (Julia)](https://openbiox.github.io/Bizard/Julia/RadarPlot.html)
+- [Survival Curve (Julia)](https://openbiox.github.io/Bizard/Julia/SurvivalPlot.html)
+- [ROC & PR (Julia)](https://openbiox.github.io/Bizard/Julia/RocPrPlot.html)
+- [Forest Plot (Julia)](https://openbiox.github.io/Bizard/Julia/ForestPlot.html)
+- [Manhattan & QQ (Julia)](https://openbiox.github.io/Bizard/Julia/ManhattanPlot.html)
+- [Faceted Plots (Julia)](https://openbiox.github.io/Bizard/Julia/FacetPlot.html)
+- [Multi-Panel Figures (Julia)](https://openbiox.github.io/Bizard/Julia/GridLayoutPlot.html)
+- [Annotated Heatmap (Julia)](https://openbiox.github.io/Bizard/Julia/AnnotatedHeatmap.html)
 
 ## KEGGPathwayPlot
 - [KEGG Pathway Plot](https://openbiox.github.io/Bizard/Omics/KeggPathwayPlot.html#fig-1-1)
@@ -642,6 +681,13 @@
 - [Direction Rotation of Multiple Volcano Plot](https://openbiox.github.io/Bizard/Omics/MultiVolcanoPlot.html#direction-of-rotation)
 - [Polar Coordinates of Multiple Volcano Plot](https://openbiox.github.io/Bizard/Omics/MultiVolcanoPlot.html#polar-coordinates)
 
+## MutationOncoplot
+- [Basic Mutation Landscape Oncoplot](https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.1BasicOncoplot)
+- [Oncoplot split by molecular subtype with mutation burden bars](https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.2CohortOncoplot)
+- [Oncoplot with genes grouped by signaling pathway](https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.3PathwayOncoplot)
+- [Basic maftools oncoplot of the same cohort](https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.4MaftoolsOncoplot)
+- [maftools oncoplot annotated and sorted by molecular subtype](https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.5MaftoolsCohortOncoplot)
+
 ## NetworkPlot
 - [Build Network Plot](https://openbiox.github.io/Bizard/Omics/NetworkPlot.html#build-network)
 - [Add Annotation to Nework Plot](https://openbiox.github.io/Bizard/Omics/NetworkPlot.html#add-annotation)
@@ -752,6 +798,129 @@
 - [Basic Volcano Plot](https://openbiox.github.io/Bizard/Python/VolcanoPlot.html#fig-py-volcano-basic)
 - [Volcano Plot with Top Gene Labels](https://openbiox.github.io/Bizard/Python/VolcanoPlot.html#fig-py-volcano-labels)
 - [Enhanced Volcano Plot with Highlighted Regions](https://openbiox.github.io/Bizard/Python/VolcanoPlot.html#fig-py-volcano-enhanced)
+- [Bar Plot (Python)](https://openbiox.github.io/Bizard/Python/BarPlot.html)
+- [Box Plot (Python)](https://openbiox.github.io/Bizard/Python/BoxPlot.html)
+- [Histogram & Density Plot (Python)](https://openbiox.github.io/Bizard/Python/HistKdePlot.html)
+- [Line Plot (Python)](https://openbiox.github.io/Bizard/Python/LinePlot.html)
+- [Ridgeline Plot (Python)](https://openbiox.github.io/Bizard/Python/RidgelinePlot.html)
+- [Raincloud Plot (Python)](https://openbiox.github.io/Bizard/Python/RaincloudPlot.html)
+- [Lollipop & Dumbbell Plot (Python)](https://openbiox.github.io/Bizard/Python/LollipopPlot.html)
+- [Joint & Pair Plot (Python)](https://openbiox.github.io/Bizard/Python/JointPairPlot.html)
+- [Bar plot of mean response by dose group with SEM error bars](https://openbiox.github.io/Bizard/Python/BarPlot.html#fig-py-bar-basic)
+- [Grouped bar plot with a second experimental factor](https://openbiox.github.io/Bizard/Python/BarPlot.html#fig-py-bar-grouped)
+- [Stacked bar plot of cell-type composition per sample](https://openbiox.github.io/Bizard/Python/BarPlot.html#fig-py-bar-stacked)
+- [100% stacked bar plot of relative cell-type composition](https://openbiox.github.io/Bizard/Python/BarPlot.html#fig-py-bar-stacked100)
+- [Box plot of serum biomarker across genotypes](https://openbiox.github.io/Bizard/Python/BoxPlot.html#fig-py-box-basic)
+- [Box plot overlaid with individual data points](https://openbiox.github.io/Bizard/Python/BoxPlot.html#fig-py-box-points)
+- [Grouped box plot with a sex factor](https://openbiox.github.io/Bizard/Python/BoxPlot.html#fig-py-box-grouped)
+- [Notched box plot; notches approximate the median 95% CI](https://openbiox.github.io/Bizard/Python/BoxPlot.html#fig-py-box-notched)
+- [Histogram of simulated expression values](https://openbiox.github.io/Bizard/Python/HistKdePlot.html#fig-py-hist-basic)
+- [Histogram with a kernel density overlay](https://openbiox.github.io/Bizard/Python/HistKdePlot.html#fig-py-hist-kde)
+- [Overlaid density curves for control vs stimulated conditions](https://openbiox.github.io/Bizard/Python/HistKdePlot.html#fig-py-kde-groups)
+- [Empirical cumulative distribution functions by condition](https://openbiox.github.io/Bizard/Python/HistKdePlot.html#fig-py-ecdf)
+- [Joint plot of CD4 vs CD8 with marginal distributions](https://openbiox.github.io/Bizard/Python/JointPairPlot.html#fig-py-joint-scatter)
+- [Joint plot with KDE contours and density marginals](https://openbiox.github.io/Bizard/Python/JointPairPlot.html#fig-py-joint-kde)
+- [Pair plot of iris measurements by species (corner layout)](https://openbiox.github.io/Bizard/Python/JointPairPlot.html#fig-py-pairplot)
+- [Mean tumor size per week for the two treatment arms](https://openbiox.github.io/Bizard/Python/LinePlot.html#fig-py-line-basic)
+- [Group mean with bootstrapped 95% confidence band](https://openbiox.github.io/Bizard/Python/LinePlot.html#fig-py-line-ci)
+- [Individual growth curves (thin) with the group mean (bold)](https://openbiox.github.io/Bizard/Python/LinePlot.html#fig-py-line-spaghetti)
+- [Pathway enrichment ranked as a horizontal lollipop plot](https://openbiox.github.io/Bizard/Python/LollipopPlot.html#fig-py-lollipop-basic)
+- [Vertical lollipop plot of the enrichment scores](https://openbiox.github.io/Bizard/Python/LollipopPlot.html#fig-py-lollipop-vertical)
+- [Dumbbell plot comparing log2 fold changes between two conditions](https://openbiox.github.io/Bizard/Python/LollipopPlot.html#fig-py-dumbbell)
+- [Raincloud plot of response intensities across stimulation conditions](https://openbiox.github.io/Bizard/Python/RaincloudPlot.html#fig-py-rain-basic)
+- [Horizontal raincloud plot with long category labels](https://openbiox.github.io/Bizard/Python/RaincloudPlot.html#fig-py-rain-horizontal)
+- [Raincloud plot split by a responder subgroup](https://openbiox.github.io/Bizard/Python/RaincloudPlot.html#fig-py-rain-grouped)
+- [Marker-expression distribution across eight cell clusters](https://openbiox.github.io/Bizard/Python/RidgelinePlot.html#fig-py-ridge-basic)
+- [Ridgeline with colormap-encoded order and fading fill](https://openbiox.github.io/Bizard/Python/RidgelinePlot.html#fig-py-ridge-fade)
+- [Histogram-based ridgeline (binned counts per cluster)](https://openbiox.github.io/Bizard/Python/RidgelinePlot.html#fig-py-ridge-hist)
+- [Pie & Donut (Python)](https://openbiox.github.io/Bizard/Python/PieDonutPlot.html)
+- [Area & Streamgraph (Python)](https://openbiox.github.io/Bizard/Python/AreaPlot.html)
+- [Venn Diagram (Python)](https://openbiox.github.io/Bizard/Python/VennPlot.html)
+- [UpSet Plot (Python)](https://openbiox.github.io/Bizard/Python/UpSetPlot.html)
+- [PCA Plot (Python)](https://openbiox.github.io/Bizard/Python/PcaPlot.html)
+- [Correlogram (Python)](https://openbiox.github.io/Bizard/Python/CorrelogramPlot.html)
+- [Bivariate Density (Python)](https://openbiox.github.io/Bizard/Python/BivariateDensityPlot.html)
+- [Significance Annotation (Python)](https://openbiox.github.io/Bizard/Python/SignificanceAnnotation.html)
+- [CD8 T-cell counts over the vaccination course](https://openbiox.github.io/Bizard/Python/AreaPlot.html#fig-py-area-single)
+- [Stacked lymphocyte counts across the study weeks](https://openbiox.github.io/Bizard/Python/AreaPlot.html#fig-py-area-stacked)
+- [Streamgraph of lymphocyte composition (wiggle baseline)](https://openbiox.github.io/Bizard/Python/AreaPlot.html#fig-py-area-stream)
+- [Filled 2D density of a 20,000-cell cytometry sample](https://openbiox.github.io/Bizard/Python/BivariateDensityPlot.html#fig-py-bidensity-kde)
+- [Hexbin counts of the same cytometry sample](https://openbiox.github.io/Bizard/Python/BivariateDensityPlot.html#fig-py-bidensity-hexbin)
+- [Per-population contours with a 2% scatter overlay](https://openbiox.github.io/Bizard/Python/BivariateDensityPlot.html#fig-py-bidensity-contour)
+- [Marker-panel correlogram (lower triangle, annotated coefficients)](https://openbiox.github.io/Bizard/Python/CorrelogramPlot.html#fig-py-corr-masked)
+- [Cluster-ordered correlogram of the marker panel](https://openbiox.github.io/Bizard/Python/CorrelogramPlot.html#fig-py-corr-cluster)
+- [PCA scores of the three cohorts on the first two components](https://openbiox.github.io/Bizard/Python/PcaPlot.html#fig-py-pca-scores)
+- [PCA biplot: scores by cohort with the top-8 loading genes](https://openbiox.github.io/Bizard/Python/PcaPlot.html#fig-py-pca-biplot)
+- [Explained variance per component (bar) with cumulative share (line)](https://openbiox.github.io/Bizard/Python/PcaPlot.html#fig-py-pca-scree)
+- [Cell-type composition of a PBMC sample as a pie chart](https://openbiox.github.io/Bizard/Python/PieDonutPlot.html#fig-py-pie-basic)
+- [Donut chart with the sample total annotated in the center](https://openbiox.github.io/Bizard/Python/PieDonutPlot.html#fig-py-donut-center)
+- [Donut chart highlighting one expanded cell type](https://openbiox.github.io/Bizard/Python/PieDonutPlot.html#fig-py-pie-highlight)
+- [Box plot with one Mann–Whitney comparison marked by a bracket](https://openbiox.github.io/Bizard/Python/SignificanceAnnotation.html#fig-py-sig-pair)
+- [Dose arms vs vehicle with Bonferroni-adjusted significance stars](https://openbiox.github.io/Bizard/Python/SignificanceAnnotation.html#fig-py-sig-multiple)
+- [Intersection of gene coverage across four omics platforms](https://openbiox.github.io/Bizard/Python/UpSetPlot.html#fig-py-upset-basic)
+- [UpSet plot sorted by coverage degree with percentage labels](https://openbiox.github.io/Bizard/Python/UpSetPlot.html#fig-py-upset-degree)
+- [Overlap between drug A and drug B target sets](https://openbiox.github.io/Bizard/Python/VennPlot.html#fig-py-venn2)
+- [Overlap of drug targets with the disease DEG set](https://openbiox.github.io/Bizard/Python/VennPlot.html#fig-py-venn3)
+- [MA Plot (Python)](https://openbiox.github.io/Bizard/Python/MAPlot.html)
+- [Manhattan & QQ (Python)](https://openbiox.github.io/Bizard/Python/ManhattanPlot.html)
+- [Survival Curve (Python)](https://openbiox.github.io/Bizard/Python/SurvivalPlot.html)
+- [Forest Plot (Python)](https://openbiox.github.io/Bizard/Python/ForestPlot.html)
+- [ROC & PR (Python)](https://openbiox.github.io/Bizard/Python/RocPrPlot.html)
+- [Confusion Matrix (Python)](https://openbiox.github.io/Bizard/Python/ConfusionMatrixPlot.html)
+- [Enrichment Plot (Python)](https://openbiox.github.io/Bizard/Python/EnrichmentPlot.html)
+- [Complex Heatmap (Python)](https://openbiox.github.io/Bizard/Python/ComplexHeatmap.html)
+- [Circos & Chord (Python)](https://openbiox.github.io/Bizard/Python/CircosPlot.html)
+- [Marker sharing between three immune cell types as a chord diagram](https://openbiox.github.io/Bizard/Python/CircosPlot.html#fig-py-circos-chord)
+- [Circos sectors with a per-sector bar track](https://openbiox.github.io/Bizard/Python/CircosPlot.html#fig-py-circos-tracks)
+- [Clustered expression heatmap with cohort and sex annotations](https://openbiox.github.io/Bizard/Python/ComplexHeatmap.html#fig-py-cm-annotated)
+- [Clustered heatmap with per-gene row labels](https://openbiox.github.io/Bizard/Python/ComplexHeatmap.html#fig-py-cm-split)
+- [Confusion matrix of the three-class lymphoma classifier (counts)](https://openbiox.github.io/Bizard/Python/ConfusionMatrixPlot.html#fig-py-cm-counts)
+- [Row-normalized confusion matrix annotated with counts and shares](https://openbiox.github.io/Bizard/Python/ConfusionMatrixPlot.html#fig-py-cm-normalized)
+- [Enriched pathways ranked by -log10 adjusted p-value](https://openbiox.github.io/Bizard/Python/EnrichmentPlot.html#fig-py-enrich-bar)
+- [Enrichment dot plot: ratio by colour, count by size](https://openbiox.github.io/Bizard/Python/EnrichmentPlot.html#fig-py-enrich-dot)
+- [Meta-analysis forest plot with inverse-variance pooled diamond](https://openbiox.github.io/Bizard/Python/ForestPlot.html#fig-py-forest-basic)
+- [Forest plot with subgroup headers](https://openbiox.github.io/Bizard/Python/ForestPlot.html#fig-py-forest-subgroup)
+- [MA plot with significance colouring and fold-change guides](https://openbiox.github.io/Bizard/Python/MAPlot.html#fig-py-ma-basic)
+- [MA plot with the top-6 up-regulated genes labelled](https://openbiox.github.io/Bizard/Python/MAPlot.html#fig-py-ma-labeled)
+- [Manhattan plot of the simulated GWAS with Bonferroni and suggestive lines](https://openbiox.github.io/Bizard/Python/ManhattanPlot.html#fig-py-manhattan)
+- [QQ plot of GWAS p-values with the genomic inflation factor](https://openbiox.github.io/Bizard/Python/ManhattanPlot.html#fig-py-qq)
+- [ROC curve with the chance diagonal and AUC](https://openbiox.github.io/Bizard/Python/RocPrPlot.html#fig-py-roc)
+- [Precision-recall curve with average precision and prevalence baseline](https://openbiox.github.io/Bizard/Python/RocPrPlot.html#fig-py-pr)
+- [Kaplan–Meier overall survival with 95% confidence bands](https://openbiox.github.io/Bizard/Python/SurvivalPlot.html#fig-py-km-basic)
+- [KM curves annotated with medians and the log-rank test](https://openbiox.github.io/Bizard/Python/SurvivalPlot.html#fig-py-km-annotated)
+- [Faceted Plots (Python)](https://openbiox.github.io/Bizard/Python/FacetGridPlot.html)
+- [Multi-Panel Figures (Python)](https://openbiox.github.io/Bizard/Python/MultiPanelPlot.html)
+- [Publication Style & Export (Python)](https://openbiox.github.io/Bizard/Python/PublicationStyle.html)
+- [Response trajectories faceted by genotype, coloured by arm](https://openbiox.github.io/Bizard/Python/FacetGridPlot.html#fig-py-facet-rel)
+- [Score distributions by week, faceted by genotype](https://openbiox.github.io/Bizard/Python/FacetGridPlot.html#fig-py-facet-cat)
+- [FacetGrid mapping a custom histogram+KDE panel function](https://openbiox.github.io/Bizard/Python/FacetGridPlot.html#fig-py-facet-grid)
+- [GridSpec composite: main scatter with top and right marginals](https://openbiox.github.io/Bizard/Python/MultiPanelPlot.html#fig-py-grid-marginals)
+- [Two lettered subfigures sharing one exported file](https://openbiox.github.io/Bizard/Python/MultiPanelPlot.html#fig-py-subfig-letters)
+- [House-style bar plot: 89 mm width, 7 pt fonts, outward ticks](https://openbiox.github.io/Bizard/Python/PublicationStyle.html#fig-py-style-rcparams)
+- [The same data under the SciencePlots 'science' + 'nature' styles](https://openbiox.github.io/Bizard/Python/PublicationStyle.html#fig-py-style-scienceplots)
+- [Sankey Diagram (Python)](https://openbiox.github.io/Bizard/Python/SankeyDiagram.html)
+- [Parallel Categories (Python)](https://openbiox.github.io/Bizard/Python/ParallelCategoriesPlot.html)
+- [Choropleth Map (Python)](https://openbiox.github.io/Bizard/Python/ChoroplethMap.html)
+- [scRNA-seq UMAP (Python)](https://openbiox.github.io/Bizard/Python/ScrnaUmapPlot.html)
+- [scRNA-seq Dot Plot (Python)](https://openbiox.github.io/Bizard/Python/ScrnaDotPlot.html)
+- [scRNA-seq Stacked Violin (Python)](https://openbiox.github.io/Bizard/Python/ScrnaStackedViolin.html)
+- [GSEA Running-Score (Python)](https://openbiox.github.io/Bizard/Python/GseaPlot.html)
+- [Oncoprint (Python)](https://openbiox.github.io/Bizard/Python/OncoprintPlot.html)
+- [Study enrolment per million population by country](https://openbiox.github.io/Bizard/Python/ChoroplethMap.html#fig-py-choropleth)
+- [Participating countries shaded; non-participants left grey](https://openbiox.github.io/Bizard/Python/ChoroplethMap.html#fig-py-choropleth-gap)
+- [GSEA running-score plot: ranked statistics, ES curve and hit rug](https://openbiox.github.io/Bizard/Python/GseaPlot.html#fig-py-gsea)
+- [Running ES for two gene sets on the same ranked list](https://openbiox.github.io/Bizard/Python/GseaPlot.html#fig-py-gsea-two)
+- [Alteration landscape across 12 drivers in 80 tumours](https://openbiox.github.io/Bizard/Python/OncoprintPlot.html#fig-py-oncoprint)
+- [Oncoprint emphasising truncating alterations](https://openbiox.github.io/Bizard/Python/OncoprintPlot.html#fig-py-oncoprint-outline)
+- [Patient flows across biomarker, arm, response and toxicity](https://openbiox.github.io/Bizard/Python/ParallelCategoriesPlot.html#fig-py-parcats)
+- [Same flows ordered so the dominant paths draw last](https://openbiox.github.io/Bizard/Python/ParallelCategoriesPlot.html#fig-py-parcats-sorted)
+- [Patient flow from diagnosis to outcome (n = 300)](https://openbiox.github.io/Bizard/Python/SankeyDiagram.html#fig-py-sankey)
+- [Marker expression across populations: size = fraction expressing, colour = mean level](https://openbiox.github.io/Bizard/Python/ScrnaDotPlot.html#fig-py-dotplot)
+- [Top-3 ranked markers per population](https://openbiox.github.io/Bizard/Python/ScrnaDotPlot.html#fig-py-dotplot-ranked)
+- [Marker expression distributions per population](https://openbiox.github.io/Bizard/Python/ScrnaStackedViolin.html#fig-py-stacked-violin)
+- [Transposed layout: violins per gene across populations](https://openbiox.github.io/Bizard/Python/ScrnaStackedViolin.html#fig-py-stacked-violin-swap)
+- [UMAP of the simulated PBMC populations, coloured by cell type](https://openbiox.github.io/Bizard/Python/ScrnaUmapPlot.html#fig-py-umap-clusters)
+- [UMAP coloured by expression of the B-cell marker Gene15](https://openbiox.github.io/Bizard/Python/ScrnaUmapPlot.html#fig-py-umap-feature)
 
 ## Ranking (排序)
 - [Basic Bar Plot](https://openbiox.github.io/Bizard/Ranking/BarPlot.html#fig-BasicPlot)
@@ -862,6 +1031,11 @@
 - [Regression Analysis Table](https://openbiox.github.io/Bizard/Clinics/RegressionTable.html#fig-6.1Merge)
 - [Regression Analysis Table](https://openbiox.github.io/Bizard/Clinics/RegressionTable.html#fig-6.2Merge)
 
+## SamplingMap
+- [Basic sampling site map](https://openbiox.github.io/Bizard/Omics/SamplingMap.html#fig-1.1BasicSamplingMap)
+- [Sampling map with counts in the labels](https://openbiox.github.io/Bizard/Omics/SamplingMap.html#fig-1.2LabelledSamplingMap)
+- [World view of the sampling sites](https://openbiox.github.io/Bizard/Omics/SamplingMap.html#fig-1.3WorldSamplingMap)
+
 ## SankeyBubblePlot
 - [Sankey Diagram](https://openbiox.github.io/Bizard/Omics/SankeyBubblePlot.html#fig-1.1Sankey)
 - [Bubble Plot](https://openbiox.github.io/Bizard/Omics/SankeyBubblePlot.html#fig-2.1Bubble)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openbiox/bizard-mcp",
-  "version": "0.1.3",
+  "version": "0.2.0",
   "description": "MCP server for the Bizard biomedical visualization atlas: search, adapt, cite, and contribute chart tutorials",
   "type": "module",
   "engines": { "node": ">=20" },