@openbiox/bizard-mcp 0.1.2 → 0.1.4

package/README.md

@@ -11,28 +11,41 @@ degrades gracefully by environment). Content comes from a bundle generated by
 CI from the same sources as the website and `SKILL.md`, so all three never
 drift. The server never executes plotting code — the host AI does.
 
-## Quickstart (local, stdio)
+If Bizard helps your research, please cite: Li, K., Zheng, H., et al. (2026).
+Bizard: A Community-Driven Platform for Accelerating and Enhancing Biomedical
+Data Visualization. *iMetaMed*, e70038. <https://doi.org/10.1002/imm3.70038>
+
+## Quickstart
+
+No install at all — connect to the [public hosted instance](#public-hosted-instance-no-install-required)
+(pure Streamable HTTP, works with any MCP-capable agent).
+
+Local, stdio (works offline — an npm-shipped content snapshot backs everything up):
 
 ```bash
 npx @openbiox/bizard-mcp
 ```
 
-Register it with Claude Code:
+Register the local server with Claude Code:
 
 ```bash
 claude mcp add bizard -- npx @openbiox/bizard-mcp
 ```
 
-Works offline: an npm-shipped content snapshot backs everything up.
+Hosted instance with Claude Code:
+
+```bash
+claude mcp add --transport http bizard http://biotree.top:38123/bizard-mcp/mcp
+```
 
 ## Tools
 
 | Tool | Purpose |
 |------|---------|
 | `bizard_search` | Bilingual weighted search over the chart gallery; adjacent-category suggestions on zero hits |
-| `bizard_list_categories` | Category tree (12 Level-1 categories with Chinese/English aliases and counts) |
-| `bizard_get_tutorial` | Structured tutorial content: sections, setup dependencies, data description, key parameters |
-| `bizard_get_code` | Runnable tutorial code with package list, install guard, and example-data URLs |
+| `bizard_list_categories` | All 36 chart categories with per-category chart counts (bilingual names where available) |
+| `bizard_get_tutorial` | Chart metadata: packages, example-data URLs, available languages, tutorial link |
+| `bizard_get_code` | Runnable tutorial code with package list, example-data URLs, and license notice |
 | `bizard_adapt_guidance` | Data-shape checks, dependency prep, parameter mapping, failure modes, alternatives |
 | `bizard_cite` | Bizard paper + tutorial citation (bibtex/text/json) with CC-BY-NC-4.0 license notice |
 | `bizard_contribute_check` | Validate a draft against the contribution template; preview points (issue #4) |
@@ -48,6 +61,33 @@ One package, two transports:
 - **Local (stdio, default)**: `npx @openbiox/bizard-mcp`. Full capability; contribution runs at level 1/2 when local credentials exist.
 - **Hosted (Streamable HTTP)**: `npx @openbiox/bizard-mcp --http`. Port via `BIZARD_HTTP_PORT` (default 3000). Anonymous, stateless — each POST to `/mcp` gets a fresh transport. Per-IP token-bucket rate limit (60 req/min; 429 with `Retry-After`). Contribution runs at level 3 (no credentials on the server).
 
+### Public hosted instance (no install required)
+
+A community instance is deployed by the Bizard team. It speaks standard
+Streamable HTTP, so **any MCP-capable agent** can connect — Claude Code,
+Cursor, Cline, Windsurf, VS Code Copilot Chat, custom agent frameworks —
+with no local install. It may also be faster than an npm-based setup for
+users in mainland China.
+
+Most MCP clients accept a JSON server entry:
+
+```json
+{
+  "mcpServers": {
+    "bizard": { "type": "http", "url": "http://biotree.top:38123/bizard-mcp/mcp" }
+  }
+}
+```
+
+Claude Code accepts it from the CLI too:
+
+```bash
+claude mcp add --transport http bizard http://biotree.top:38123/bizard-mcp/mcp
+```
+
+Same anonymous, stateless, rate-limited behavior as the self-hosted HTTP
+mode; contribution runs at level 3 (the instance holds no credentials).
+
 ## Contribution credential degradation
 
 `bizard_contribute_submit` probes the environment on every call and states
@@ -55,7 +95,7 @@ which level it used — never silently failing:
 
 | Level | Condition | Behavior |
 |-------|-----------|----------|
-| 1 | `gh` CLI installed and logged in | Creates issue (or PR when `asPR`) as the user |
+| 1 | `gh` CLI installed and logged in | Creates the issue as your GitHub user (PR submission is planned for a future release) |
 | 2 | No `gh`, but `GITHUB_TOKEN` set | GitHub API submission, limited by token scope |
 | 3 | Neither (typical for hosted) | Returns formatted draft + pre-filled `issues/new?title=&body=` deep-link |
 

package/dist/prompts.js

@@ -13,7 +13,8 @@ export function registerPrompts(server) {
 2. Call bizard_search with 2-3 keyword variants (EN and zh).
 3. Compare the top hits on: data types required, message emphasis, aesthetics.
 4. Recommend ONE chart plus 2 alternatives, with tutorial URLs from the results.
-5. Remind the user that code should be adapted to their data (offer the adapt prompt).`,
+5. Remind the user that code should be adapted to their data (offer the adapt prompt).
+6. When the user adopts a chart from Bizard, remind them to cite the Bizard paper (Li et al., iMetaMed 2026, doi:10.1002/imm3.70038).`,
                 },
             }],
     }));
@@ -33,7 +34,8 @@ export function registerPrompts(server) {
 2. FIRST inspect my data (str/df.info/head) — do not assume column names.
 3. Rewrite the tutorial code from bizard_get_code minimally: only parameter and column changes.
 4. Run the adapted code, show the plot, and self-check against the guidance's failure modes.
-5. If a step fails, switch to the troubleshoot flow before improvising.`,
+5. If a step fails, switch to the troubleshoot flow before improvising.
+6. When the adapted figure is used in the user's work, remind them to cite the Bizard paper (Li et al., iMetaMed 2026, doi:10.1002/imm3.70038).`,
                 },
             }],
     }));

package/dist/server.js

@@ -13,9 +13,17 @@ const QUERY_MAX_CHARS = 4000;
 export const NO_BUNDLE_ERROR = "bizard-mcp: bundle snapshot unavailable. The maintainer must run " +
     "`npm run build:bundle` (or CI) to generate src/snapshot/bundle.json, then rebuild.";
 function json(value, note) {
-    const payload = note === null || note === undefined
-        ? { ...value }
-        : { note, ...value };
+    // Arrays must be serialized as arrays: spreading an array into an object
+    // literal ({...arr}) yields numeric-string keys and breaks client-side
+    // .map()/.length. Wrap noted arrays as {note, items} so `.note` stays
+    // accessible for the one-time update notice (see notice-wiring tests).
+    let payload;
+    if (note === null || note === undefined) {
+        payload = Array.isArray(value) ? value : { ...value };
+    }
+    else {
+        payload = Array.isArray(value) ? { note, items: value } : { note, ...value };
+    }
     return {
         content: [{
                 type: "text",
@@ -30,7 +38,7 @@ function bundleError() {
     };
 }
 /** Constant server identity — never derives from bundle state. */
-const SERVER_IDENTITY = { name: "bizard-mcp", version: "0.1.2" };
+const SERVER_IDENTITY = { name: "bizard-mcp", version: "0.1.4" };
 export function createBizardServer(source, notices, opts) {
     const getBundle = () => {
         if (source === null)

package/dist/snapshot/bundle.json

@@ -2,7 +2,7 @@
   "meta": {
     "siteVersion": "",
     "bundleVersion": 1,
-    "generatedAt": "2026-10-16T06:47:43.560645+00:00",
+    "generatedAt": "2026-10-16T16:56:06.902254+00:00",
     "license": "CC-BY-NC-4.0"
   },
   "categories": [
@@ -56,6 +56,11 @@
       "nameZh": null,
       "count": 61
     },
+    {
+      "name": "FcFcPlot",
+      "nameZh": null,
+      "count": 3
+    },
     {
       "name": "GeneStructurePlot",
       "nameZh": null,
@@ -121,6 +126,11 @@
       "nameZh": null,
       "count": 6
     },
+    {
+      "name": "MutationOncoplot",
+      "nameZh": null,
+      "count": 3
+    },
     {
       "name": "NetworkPlot",
       "nameZh": null,
@@ -12427,6 +12437,96 @@
       "codeRefs": [
         "python"
       ]
+    },
+    {
+      "id": "FcFcPlot-817",
+      "name": "Basic FC-FC Scatter Plot",
+      "nameZh": "基础 FC-FC 散点图",
+      "type": "FC-FC Scatter Plot",
+      "level1": "OMICS",
+      "level2": "FcFcPlot",
+      "tutorialUrl": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html#fig-1.1BasicFcFc",
+      "tutorialUrlZh": "https://openbiox.github.io/Bizard/zh/Omics/FcFcPlot.html#fig-1.1BasicFcFc",
+      "imageUrl": "https://openbiox.github.io/Bizard/Omics/FcFcPlot_files/figure-html/fig-1.1BasicFcFc-1.png",
+      "description": "Basic FC-FC scatter plot with fold-change threshold lines and a reference diagonal built with ggplot2",
+      "codeRefs": [
+        "r"
+      ]
+    },
+    {
+      "id": "FcFcPlot-818",
+      "name": "Color points by significance category",
+      "nameZh": "按显著性类别着色",
+      "type": "FC-FC Scatter Plot",
+      "level1": "OMICS",
+      "level2": "FcFcPlot",
+      "tutorialUrl": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html#fig-1.2CategoryFcFc",
+      "tutorialUrlZh": "https://openbiox.github.io/Bizard/zh/Omics/FcFcPlot.html#fig-1.2CategoryFcFc",
+      "imageUrl": "https://openbiox.github.io/Bizard/Omics/FcFcPlot_files/figure-html/fig-1.2CategoryFcFc-1.png",
+      "description": "Points colored by significance category — shared / subset-specific / discordant markers",
+      "codeRefs": [
+        "r"
+      ]
+    },
+    {
+      "id": "FcFcPlot-819",
+      "name": "FC-FC scatter plot with significance-scaled points and curated gene labels",
+      "nameZh": "点大小编码显著性并标注基因的 FC-FC 散点图",
+      "type": "FC-FC Scatter Plot",
+      "level1": "OMICS",
+      "level2": "FcFcPlot",
+      "tutorialUrl": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html#fig-1.3LabelFcFc",
+      "tutorialUrlZh": "https://openbiox.github.io/Bizard/zh/Omics/FcFcPlot.html#fig-1.3LabelFcFc",
+      "imageUrl": "https://openbiox.github.io/Bizard/Omics/FcFcPlot_files/figure-html/fig-1.3LabelFcFc-1.png",
+      "description": "Point size encodes statistical significance and genes at the extremes and top shared markers are labeled",
+      "codeRefs": [
+        "r"
+      ]
+    },
+    {
+      "id": "MutationOncoplot-820",
+      "name": "Basic Mutation Landscape Oncoplot",
+      "nameZh": "基础基因突变全景瀑布图",
+      "type": "Mutation Landscape Oncoplot",
+      "level1": "OMICS",
+      "level2": "MutationOncoplot",
+      "tutorialUrl": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.1BasicOncoplot",
+      "tutorialUrlZh": "https://openbiox.github.io/Bizard/zh/Omics/MutationOncoplot.html#fig-1.1BasicOncoplot",
+      "imageUrl": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot_files/figure-html/fig-1.1BasicOncoplot-1.png",
+      "description": "Basic oncoplot showing the simulated cohort mutation matrix with per-gene frequencies and alteration counts",
+      "codeRefs": [
+        "r"
+      ]
+    },
+    {
+      "id": "MutationOncoplot-821",
+      "name": "Oncoplot split by molecular subtype with mutation burden bars",
+      "nameZh": "按分子亚型拆分并带突变负荷条的 oncoplot",
+      "type": "Mutation Landscape Oncoplot",
+      "level1": "OMICS",
+      "level2": "MutationOncoplot",
+      "tutorialUrl": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.2CohortOncoplot",
+      "tutorialUrlZh": "https://openbiox.github.io/Bizard/zh/Omics/MutationOncoplot.html#fig-1.2CohortOncoplot",
+      "imageUrl": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot_files/figure-html/fig-1.2CohortOncoplot-1.png",
+      "description": "Samples split by molecular subtype with a top barplot of each sample's total mutation count",
+      "codeRefs": [
+        "r"
+      ]
+    },
+    {
+      "id": "MutationOncoplot-822",
+      "name": "Oncoplot with genes grouped by signaling pathway",
+      "nameZh": "按信号通路分组基因的 oncoplot",
+      "type": "Mutation Landscape Oncoplot",
+      "level1": "OMICS",
+      "level2": "MutationOncoplot",
+      "tutorialUrl": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html#fig-1.3PathwayOncoplot",
+      "tutorialUrlZh": "https://openbiox.github.io/Bizard/zh/Omics/MutationOncoplot.html#fig-1.3PathwayOncoplot",
+      "imageUrl": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot_files/figure-html/fig-1.3PathwayOncoplot-1.png",
+      "description": "The same cohort with genes grouped by signaling pathway for a functional reading of the landscape",
+      "codeRefs": [
+        "r"
+      ]
     }
   ],
   "codeSnippets": [
@@ -168932,6 +169032,315 @@
       ],
       "dataUrls": [],
       "sourceAnchor": "https://openbiox.github.io/Bizard/Python/VolcanoPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-817",
+      "lang": "r",
+      "code": "# Load the PBMC marker gene table\ndata(\"pbmc.markers\")\n\n# Marker statistics of the two monocyte subsets\ncd14 <- pbmc.markers |>\n  filter(cluster == \"CD14+ Mono\") |>\n  select(gene, avg_log2FC, p_val_adj)\n\nfcgr3a <- pbmc.markers |>\n  filter(cluster == \"FCGR3A+ Mono\") |>\n  select(gene, avg_log2FC, p_val_adj)\n\n# Join by gene: 546 genes are markers in both subsets\nfc_fc <- inner_join(cd14, fcgr3a, by = \"gene\", suffix = c(\"_cd14\", \"_fcgr3a\"))\n\n# Classify each gene and compute the plotting score\nfc_cut <- 0.5\np_cut <- 0.05\nfc_fc <- fc_fc |>\n  mutate(\n    sig_cd14 = p_val_adj_cd14 < p_cut & abs(avg_log2FC_cd14) >= fc_cut,\n    sig_fcgr3a = p_val_adj_fcgr3a < p_cut & abs(avg_log2FC_fcgr3a) >= fc_cut,\n    category = case_when(\n      sig_cd14 & sig_fcgr3a & sign(avg_log2FC_cd14) == sign(avg_log2FC_fcgr3a) ~ \"Shared marker\",\n      sig_cd14 & sig_fcgr3a ~ \"Discordant\",\n      sig_cd14 ~ \"CD14+ Mono-specific\",\n      sig_fcgr3a ~ \"FCGR3A+ Mono-specific\",\n      TRUE ~ \"Not significant\"\n    ),\n    neglog10p = -log10(pmax(p_val_adj_cd14, p_val_adj_fcgr3a))\n  )\n\n# View data\nhead(fc_fc)",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-817",
+      "lang": "r",
+      "code": "ggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_abline(slope = 1, intercept = 0, linetype = \"dotted\", color = \"grey60\") +\n  geom_point(color = \"#2166AC\", size = 1.8, alpha = 0.7) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\")) +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-817",
+      "lang": "r",
+      "code": "category_colors <- c(\n  \"Shared marker\" = \"#B2182B\",\n  \"Discordant\" = \"#7B3294\",\n  \"CD14+ Mono-specific\" = \"#2166AC\",\n  \"FCGR3A+ Mono-specific\" = \"#1B9E77\",\n  \"Not significant\" = \"grey70\"\n)\n\nggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_point(aes(color = category), size = 2, alpha = 0.75) +\n  scale_color_manual(values = category_colors) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\"),\n       color = \"Category\") +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-817",
+      "lang": "r",
+      "code": "# Curated label set: discordant genes, extremes on both axes and top shared markers\nlabel_genes <- bind_rows(\n  fc_fc |> filter(category == \"Discordant\") |>\n    slice_max(abs(avg_log2FC_cd14 - avg_log2FC_fcgr3a), n = 3),\n  fc_fc |> slice_max(abs(avg_log2FC_cd14), n = 3),\n  fc_fc |> slice_max(abs(avg_log2FC_fcgr3a), n = 3),\n  fc_fc |> filter(gene == \"MS4A7\"),\n  fc_fc |> filter(category == \"Shared marker\") |>\n    slice_max(neglog10p + pmin(abs(avg_log2FC_cd14), abs(avg_log2FC_fcgr3a)), n = 6)\n) |>\n  distinct(gene, .keep_all = TRUE)\n\nggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_abline(slope = 1, intercept = 0, linetype = \"dotted\", color = \"grey60\") +\n  geom_point(aes(color = category, size = neglog10p), alpha = 0.75) +\n  scale_color_manual(values = category_colors) +\n  scale_size_continuous(range = c(0.8, 5), name = expression(-log[10](P[adj]))) +\n  geom_text_repel(data = label_genes, aes(label = gene, color = category),\n                  size = 3.1, fontface = \"italic\", max.overlaps = 40,\n                  box.padding = 0.55, segment.size = 0.25,\n                  show.legend = FALSE, seed = 1) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\"),\n       color = \"Category\") +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-818",
+      "lang": "r",
+      "code": "# Load the PBMC marker gene table\ndata(\"pbmc.markers\")\n\n# Marker statistics of the two monocyte subsets\ncd14 <- pbmc.markers |>\n  filter(cluster == \"CD14+ Mono\") |>\n  select(gene, avg_log2FC, p_val_adj)\n\nfcgr3a <- pbmc.markers |>\n  filter(cluster == \"FCGR3A+ Mono\") |>\n  select(gene, avg_log2FC, p_val_adj)\n\n# Join by gene: 546 genes are markers in both subsets\nfc_fc <- inner_join(cd14, fcgr3a, by = \"gene\", suffix = c(\"_cd14\", \"_fcgr3a\"))\n\n# Classify each gene and compute the plotting score\nfc_cut <- 0.5\np_cut <- 0.05\nfc_fc <- fc_fc |>\n  mutate(\n    sig_cd14 = p_val_adj_cd14 < p_cut & abs(avg_log2FC_cd14) >= fc_cut,\n    sig_fcgr3a = p_val_adj_fcgr3a < p_cut & abs(avg_log2FC_fcgr3a) >= fc_cut,\n    category = case_when(\n      sig_cd14 & sig_fcgr3a & sign(avg_log2FC_cd14) == sign(avg_log2FC_fcgr3a) ~ \"Shared marker\",\n      sig_cd14 & sig_fcgr3a ~ \"Discordant\",\n      sig_cd14 ~ \"CD14+ Mono-specific\",\n      sig_fcgr3a ~ \"FCGR3A+ Mono-specific\",\n      TRUE ~ \"Not significant\"\n    ),\n    neglog10p = -log10(pmax(p_val_adj_cd14, p_val_adj_fcgr3a))\n  )\n\n# View data\nhead(fc_fc)",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-818",
+      "lang": "r",
+      "code": "ggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_abline(slope = 1, intercept = 0, linetype = \"dotted\", color = \"grey60\") +\n  geom_point(color = \"#2166AC\", size = 1.8, alpha = 0.7) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\")) +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-818",
+      "lang": "r",
+      "code": "category_colors <- c(\n  \"Shared marker\" = \"#B2182B\",\n  \"Discordant\" = \"#7B3294\",\n  \"CD14+ Mono-specific\" = \"#2166AC\",\n  \"FCGR3A+ Mono-specific\" = \"#1B9E77\",\n  \"Not significant\" = \"grey70\"\n)\n\nggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_point(aes(color = category), size = 2, alpha = 0.75) +\n  scale_color_manual(values = category_colors) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\"),\n       color = \"Category\") +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-818",
+      "lang": "r",
+      "code": "# Curated label set: discordant genes, extremes on both axes and top shared markers\nlabel_genes <- bind_rows(\n  fc_fc |> filter(category == \"Discordant\") |>\n    slice_max(abs(avg_log2FC_cd14 - avg_log2FC_fcgr3a), n = 3),\n  fc_fc |> slice_max(abs(avg_log2FC_cd14), n = 3),\n  fc_fc |> slice_max(abs(avg_log2FC_fcgr3a), n = 3),\n  fc_fc |> filter(gene == \"MS4A7\"),\n  fc_fc |> filter(category == \"Shared marker\") |>\n    slice_max(neglog10p + pmin(abs(avg_log2FC_cd14), abs(avg_log2FC_fcgr3a)), n = 6)\n) |>\n  distinct(gene, .keep_all = TRUE)\n\nggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_abline(slope = 1, intercept = 0, linetype = \"dotted\", color = \"grey60\") +\n  geom_point(aes(color = category, size = neglog10p), alpha = 0.75) +\n  scale_color_manual(values = category_colors) +\n  scale_size_continuous(range = c(0.8, 5), name = expression(-log[10](P[adj]))) +\n  geom_text_repel(data = label_genes, aes(label = gene, color = category),\n                  size = 3.1, fontface = \"italic\", max.overlaps = 40,\n                  box.padding = 0.55, segment.size = 0.25,\n                  show.legend = FALSE, seed = 1) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\"),\n       color = \"Category\") +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-819",
+      "lang": "r",
+      "code": "# Load the PBMC marker gene table\ndata(\"pbmc.markers\")\n\n# Marker statistics of the two monocyte subsets\ncd14 <- pbmc.markers |>\n  filter(cluster == \"CD14+ Mono\") |>\n  select(gene, avg_log2FC, p_val_adj)\n\nfcgr3a <- pbmc.markers |>\n  filter(cluster == \"FCGR3A+ Mono\") |>\n  select(gene, avg_log2FC, p_val_adj)\n\n# Join by gene: 546 genes are markers in both subsets\nfc_fc <- inner_join(cd14, fcgr3a, by = \"gene\", suffix = c(\"_cd14\", \"_fcgr3a\"))\n\n# Classify each gene and compute the plotting score\nfc_cut <- 0.5\np_cut <- 0.05\nfc_fc <- fc_fc |>\n  mutate(\n    sig_cd14 = p_val_adj_cd14 < p_cut & abs(avg_log2FC_cd14) >= fc_cut,\n    sig_fcgr3a = p_val_adj_fcgr3a < p_cut & abs(avg_log2FC_fcgr3a) >= fc_cut,\n    category = case_when(\n      sig_cd14 & sig_fcgr3a & sign(avg_log2FC_cd14) == sign(avg_log2FC_fcgr3a) ~ \"Shared marker\",\n      sig_cd14 & sig_fcgr3a ~ \"Discordant\",\n      sig_cd14 ~ \"CD14+ Mono-specific\",\n      sig_fcgr3a ~ \"FCGR3A+ Mono-specific\",\n      TRUE ~ \"Not significant\"\n    ),\n    neglog10p = -log10(pmax(p_val_adj_cd14, p_val_adj_fcgr3a))\n  )\n\n# View data\nhead(fc_fc)",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-819",
+      "lang": "r",
+      "code": "ggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_abline(slope = 1, intercept = 0, linetype = \"dotted\", color = \"grey60\") +\n  geom_point(color = \"#2166AC\", size = 1.8, alpha = 0.7) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\")) +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-819",
+      "lang": "r",
+      "code": "category_colors <- c(\n  \"Shared marker\" = \"#B2182B\",\n  \"Discordant\" = \"#7B3294\",\n  \"CD14+ Mono-specific\" = \"#2166AC\",\n  \"FCGR3A+ Mono-specific\" = \"#1B9E77\",\n  \"Not significant\" = \"grey70\"\n)\n\nggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_point(aes(color = category), size = 2, alpha = 0.75) +\n  scale_color_manual(values = category_colors) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\"),\n       color = \"Category\") +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "FcFcPlot-819",
+      "lang": "r",
+      "code": "# Curated label set: discordant genes, extremes on both axes and top shared markers\nlabel_genes <- bind_rows(\n  fc_fc |> filter(category == \"Discordant\") |>\n    slice_max(abs(avg_log2FC_cd14 - avg_log2FC_fcgr3a), n = 3),\n  fc_fc |> slice_max(abs(avg_log2FC_cd14), n = 3),\n  fc_fc |> slice_max(abs(avg_log2FC_fcgr3a), n = 3),\n  fc_fc |> filter(gene == \"MS4A7\"),\n  fc_fc |> filter(category == \"Shared marker\") |>\n    slice_max(neglog10p + pmin(abs(avg_log2FC_cd14), abs(avg_log2FC_fcgr3a)), n = 6)\n) |>\n  distinct(gene, .keep_all = TRUE)\n\nggplot(fc_fc, aes(avg_log2FC_cd14, avg_log2FC_fcgr3a)) +\n  geom_hline(yintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_vline(xintercept = c(-fc_cut, fc_cut), linetype = \"dashed\", color = \"grey50\") +\n  geom_abline(slope = 1, intercept = 0, linetype = \"dotted\", color = \"grey60\") +\n  geom_point(aes(color = category, size = neglog10p), alpha = 0.75) +\n  scale_color_manual(values = category_colors) +\n  scale_size_continuous(range = c(0.8, 5), name = expression(-log[10](P[adj]))) +\n  geom_text_repel(data = label_genes, aes(label = gene, color = category),\n                  size = 3.1, fontface = \"italic\", max.overlaps = 40,\n                  box.padding = 0.55, segment.size = 0.25,\n                  show.legend = FALSE, seed = 1) +\n  labs(x = expression(log[2]*FC~\"(CD14+ Mono vs rest)\"),\n       y = expression(log[2]*FC~\"(FCGR3A+ Mono vs rest)\"),\n       color = \"Category\") +\n  theme_bw()",
+      "packages": [
+        "ggrepel",
+        "scRNAtoolVis",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/FcFcPlot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-820",
+      "lang": "r",
+      "code": "set.seed(2026)\n\ngenes <- c(\"TP53\", \"EGFR\", \"KRAS\", \"STK11\", \"KEAP1\", \"PIK3CA\", \"PTEN\", \"RB1\",\n           \"APC\", \"ARID1A\", \"NF1\", \"NOTCH1\", \"BRAF\", \"CDKN2A\", \"SMAD4\", \"FBXW7\",\n           \"ATM\", \"BRCA2\", \"ERBB2\", \"MET\")\ncohort <- rep(c(\"Subtype A\", \"Subtype B\"), c(35, 25))\nsamples <- sprintf(\"S%02d\", 1:60)\n\n# Subtype-specific mutation probabilities per gene\np_a <- c(.52, .34, .10, .14, .10, .10, .12, .10, .06, .22, .08, .06, .04, .10, .05, .06, .06, .05, .05, .04)\np_b <- c(.22, .08, .42, .40, .36, .14, .10, .10, .10, .06, .10, .06, .06, .10, .10, .08, .05, .05, .06, .08)\nmut_types <- c(\"Missense\", \"Nonsense\", \"Frameshift\", \"Splice_Site\", \"In_Frame\")\ntype_p <- c(.58, .14, .12, .08, .08)\n\nmutations <- map_dfr(seq_along(samples), function(i) {\n  p <- if (cohort[i] == \"Subtype A\") p_a else p_b\n  hit <- genes[runif(length(genes)) < p]\n  if (length(hit) == 0) return(NULL)\n  type <- sample(mut_types, length(hit), replace = TRUE, prob = type_p)\n  # Tumor suppressors such as TP53 can receive a second hit, shown as Multi_Hit\n  if (runif(1) < .15 && \"TP53\" %in% hit) {\n    type[hit == \"TP53\"] <- \"Multi_Hit\"\n  }\n  tibble(sample = samples[i], gene = hit, type = type)\n})\n\nhead(mutations)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-820",
+      "lang": "r",
+      "code": "# Reshape the mutation table into a gene x sample matrix; a cell holds one or\n# several alteration types separated by \";\"\ngene_levels <- names(sort(table(factor(mutations$gene, levels = genes)), decreasing = TRUE))\nmat <- matrix(\"\", nrow = length(genes), ncol = length(samples),\n              dimnames = list(genes, samples))\nfor (i in seq_len(nrow(mutations))) {\n  cell <- mat[mutations$gene[i], mutations$sample[i]]\n  mat[mutations$gene[i], mutations$sample[i]] <-\n    if (cell == \"\") mutations$type[i] else paste(cell, mutations$type[i], sep = \";\")\n}\n\n# Order samples: by subtype, then by mutation count (waterfall look)\nmut_count <- colSums(mat != \"\")\nord <- order(factor(cohort, levels = c(\"Subtype A\", \"Subtype B\")), -mut_count)\nmat <- mat[gene_levels, ord]\n\n# Annotation vectors aligned with the reordered matrix\ncohort_ordered <- factor(cohort[ord], levels = c(\"Subtype A\", \"Subtype B\"))\ntmb <- mut_count[ord]\n\n# Colors for alteration types\nmutation_colors <- c(\n  Missense = \"#3690C0\", Nonsense = \"#A50F15\", Frameshift = \"#F16913\",\n  Splice_Site = \"#6A51A3\", In_Frame = \"#31A354\", Multi_Hit = \"#252525\"\n)\n\n# One drawing function per alteration type\nrect_fun <- function(color) {\n  function(x, y, w, h) grid.rect(x, y, w * 0.9, h * 0.9, gp = gpar(fill = color, col = NA))\n}\nalter_fun <- list(\n  background = rect_fun(\"#F2F2F2\"),\n  Missense = rect_fun(mutation_colors[\"Missense\"]),\n  Nonsense = rect_fun(mutation_colors[\"Nonsense\"]),\n  Frameshift = rect_fun(mutation_colors[\"Frameshift\"]),\n  Splice_Site = rect_fun(mutation_colors[\"Splice_Site\"]),\n  In_Frame = rect_fun(mutation_colors[\"In_Frame\"]),\n  Multi_Hit = rect_fun(mutation_colors[\"Multi_Hit\"])\n)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-820",
+      "lang": "r",
+      "code": "p1 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p1)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-820",
+      "lang": "r",
+      "code": "top_annotation <- HeatmapAnnotation(\n  TMB = anno_barplot(tmb, height = unit(1.1, \"cm\"),\n                     gp = gpar(fill = \"#6A51A3\", col = NA)),\n  annotation_name_gp = gpar(fontsize = 9))\n\np2 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  column_split = cohort_ordered, column_title_gp = gpar(fontsize = 10, fontface = \"bold\"),\n  top_annotation = top_annotation,\n  bottom_annotation = HeatmapAnnotation(\n    Subtype = as.character(cohort_ordered),\n    col = list(Subtype = c(\"Subtype A\" = \"#E08214\", \"Subtype B\" = \"#5E3C99\")),\n    annotation_name_side = \"left\", annotation_name_gp = gpar(fontsize = 9)),\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p2)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-820",
+      "lang": "r",
+      "code": "pathway <- c(\n  TP53 = \"p53\", RB1 = \"p53\", CDKN2A = \"p53\",\n  EGFR = \"RTK/RAS\", ERBB2 = \"RTK/RAS\", MET = \"RTK/RAS\", KRAS = \"RTK/RAS\",\n  BRAF = \"RTK/RAS\", NF1 = \"RTK/RAS\",\n  PIK3CA = \"PI3K\", PTEN = \"PI3K\", STK11 = \"PI3K\", KEAP1 = \"PI3K\",\n  APC = \"WNT/Notch\", NOTCH1 = \"WNT/Notch\", FBXW7 = \"WNT/Notch\",\n  ARID1A = \"Chromatin\", SMAD4 = \"TGF-beta\", ATM = \"DDR\", BRCA2 = \"DDR\")\npathway_levels <- c(\"RTK/RAS\", \"PI3K\", \"p53\", \"WNT/Notch\", \"Chromatin\", \"TGF-beta\", \"DDR\")\n\np3 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  row_split = factor(pathway[gene_levels], levels = pathway_levels),\n  row_title_gp = gpar(fontsize = 9, fontface = \"bold\"), row_title_rot = 0,\n  column_split = cohort_ordered, column_title_gp = gpar(fontsize = 10, fontface = \"bold\"),\n  top_annotation = top_annotation,\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p3)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-821",
+      "lang": "r",
+      "code": "set.seed(2026)\n\ngenes <- c(\"TP53\", \"EGFR\", \"KRAS\", \"STK11\", \"KEAP1\", \"PIK3CA\", \"PTEN\", \"RB1\",\n           \"APC\", \"ARID1A\", \"NF1\", \"NOTCH1\", \"BRAF\", \"CDKN2A\", \"SMAD4\", \"FBXW7\",\n           \"ATM\", \"BRCA2\", \"ERBB2\", \"MET\")\ncohort <- rep(c(\"Subtype A\", \"Subtype B\"), c(35, 25))\nsamples <- sprintf(\"S%02d\", 1:60)\n\n# Subtype-specific mutation probabilities per gene\np_a <- c(.52, .34, .10, .14, .10, .10, .12, .10, .06, .22, .08, .06, .04, .10, .05, .06, .06, .05, .05, .04)\np_b <- c(.22, .08, .42, .40, .36, .14, .10, .10, .10, .06, .10, .06, .06, .10, .10, .08, .05, .05, .06, .08)\nmut_types <- c(\"Missense\", \"Nonsense\", \"Frameshift\", \"Splice_Site\", \"In_Frame\")\ntype_p <- c(.58, .14, .12, .08, .08)\n\nmutations <- map_dfr(seq_along(samples), function(i) {\n  p <- if (cohort[i] == \"Subtype A\") p_a else p_b\n  hit <- genes[runif(length(genes)) < p]\n  if (length(hit) == 0) return(NULL)\n  type <- sample(mut_types, length(hit), replace = TRUE, prob = type_p)\n  # Tumor suppressors such as TP53 can receive a second hit, shown as Multi_Hit\n  if (runif(1) < .15 && \"TP53\" %in% hit) {\n    type[hit == \"TP53\"] <- \"Multi_Hit\"\n  }\n  tibble(sample = samples[i], gene = hit, type = type)\n})\n\nhead(mutations)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-821",
+      "lang": "r",
+      "code": "# Reshape the mutation table into a gene x sample matrix; a cell holds one or\n# several alteration types separated by \";\"\ngene_levels <- names(sort(table(factor(mutations$gene, levels = genes)), decreasing = TRUE))\nmat <- matrix(\"\", nrow = length(genes), ncol = length(samples),\n              dimnames = list(genes, samples))\nfor (i in seq_len(nrow(mutations))) {\n  cell <- mat[mutations$gene[i], mutations$sample[i]]\n  mat[mutations$gene[i], mutations$sample[i]] <-\n    if (cell == \"\") mutations$type[i] else paste(cell, mutations$type[i], sep = \";\")\n}\n\n# Order samples: by subtype, then by mutation count (waterfall look)\nmut_count <- colSums(mat != \"\")\nord <- order(factor(cohort, levels = c(\"Subtype A\", \"Subtype B\")), -mut_count)\nmat <- mat[gene_levels, ord]\n\n# Annotation vectors aligned with the reordered matrix\ncohort_ordered <- factor(cohort[ord], levels = c(\"Subtype A\", \"Subtype B\"))\ntmb <- mut_count[ord]\n\n# Colors for alteration types\nmutation_colors <- c(\n  Missense = \"#3690C0\", Nonsense = \"#A50F15\", Frameshift = \"#F16913\",\n  Splice_Site = \"#6A51A3\", In_Frame = \"#31A354\", Multi_Hit = \"#252525\"\n)\n\n# One drawing function per alteration type\nrect_fun <- function(color) {\n  function(x, y, w, h) grid.rect(x, y, w * 0.9, h * 0.9, gp = gpar(fill = color, col = NA))\n}\nalter_fun <- list(\n  background = rect_fun(\"#F2F2F2\"),\n  Missense = rect_fun(mutation_colors[\"Missense\"]),\n  Nonsense = rect_fun(mutation_colors[\"Nonsense\"]),\n  Frameshift = rect_fun(mutation_colors[\"Frameshift\"]),\n  Splice_Site = rect_fun(mutation_colors[\"Splice_Site\"]),\n  In_Frame = rect_fun(mutation_colors[\"In_Frame\"]),\n  Multi_Hit = rect_fun(mutation_colors[\"Multi_Hit\"])\n)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-821",
+      "lang": "r",
+      "code": "p1 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p1)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-821",
+      "lang": "r",
+      "code": "top_annotation <- HeatmapAnnotation(\n  TMB = anno_barplot(tmb, height = unit(1.1, \"cm\"),\n                     gp = gpar(fill = \"#6A51A3\", col = NA)),\n  annotation_name_gp = gpar(fontsize = 9))\n\np2 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  column_split = cohort_ordered, column_title_gp = gpar(fontsize = 10, fontface = \"bold\"),\n  top_annotation = top_annotation,\n  bottom_annotation = HeatmapAnnotation(\n    Subtype = as.character(cohort_ordered),\n    col = list(Subtype = c(\"Subtype A\" = \"#E08214\", \"Subtype B\" = \"#5E3C99\")),\n    annotation_name_side = \"left\", annotation_name_gp = gpar(fontsize = 9)),\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p2)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-821",
+      "lang": "r",
+      "code": "pathway <- c(\n  TP53 = \"p53\", RB1 = \"p53\", CDKN2A = \"p53\",\n  EGFR = \"RTK/RAS\", ERBB2 = \"RTK/RAS\", MET = \"RTK/RAS\", KRAS = \"RTK/RAS\",\n  BRAF = \"RTK/RAS\", NF1 = \"RTK/RAS\",\n  PIK3CA = \"PI3K\", PTEN = \"PI3K\", STK11 = \"PI3K\", KEAP1 = \"PI3K\",\n  APC = \"WNT/Notch\", NOTCH1 = \"WNT/Notch\", FBXW7 = \"WNT/Notch\",\n  ARID1A = \"Chromatin\", SMAD4 = \"TGF-beta\", ATM = \"DDR\", BRCA2 = \"DDR\")\npathway_levels <- c(\"RTK/RAS\", \"PI3K\", \"p53\", \"WNT/Notch\", \"Chromatin\", \"TGF-beta\", \"DDR\")\n\np3 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  row_split = factor(pathway[gene_levels], levels = pathway_levels),\n  row_title_gp = gpar(fontsize = 9, fontface = \"bold\"), row_title_rot = 0,\n  column_split = cohort_ordered, column_title_gp = gpar(fontsize = 10, fontface = \"bold\"),\n  top_annotation = top_annotation,\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p3)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-822",
+      "lang": "r",
+      "code": "set.seed(2026)\n\ngenes <- c(\"TP53\", \"EGFR\", \"KRAS\", \"STK11\", \"KEAP1\", \"PIK3CA\", \"PTEN\", \"RB1\",\n           \"APC\", \"ARID1A\", \"NF1\", \"NOTCH1\", \"BRAF\", \"CDKN2A\", \"SMAD4\", \"FBXW7\",\n           \"ATM\", \"BRCA2\", \"ERBB2\", \"MET\")\ncohort <- rep(c(\"Subtype A\", \"Subtype B\"), c(35, 25))\nsamples <- sprintf(\"S%02d\", 1:60)\n\n# Subtype-specific mutation probabilities per gene\np_a <- c(.52, .34, .10, .14, .10, .10, .12, .10, .06, .22, .08, .06, .04, .10, .05, .06, .06, .05, .05, .04)\np_b <- c(.22, .08, .42, .40, .36, .14, .10, .10, .10, .06, .10, .06, .06, .10, .10, .08, .05, .05, .06, .08)\nmut_types <- c(\"Missense\", \"Nonsense\", \"Frameshift\", \"Splice_Site\", \"In_Frame\")\ntype_p <- c(.58, .14, .12, .08, .08)\n\nmutations <- map_dfr(seq_along(samples), function(i) {\n  p <- if (cohort[i] == \"Subtype A\") p_a else p_b\n  hit <- genes[runif(length(genes)) < p]\n  if (length(hit) == 0) return(NULL)\n  type <- sample(mut_types, length(hit), replace = TRUE, prob = type_p)\n  # Tumor suppressors such as TP53 can receive a second hit, shown as Multi_Hit\n  if (runif(1) < .15 && \"TP53\" %in% hit) {\n    type[hit == \"TP53\"] <- \"Multi_Hit\"\n  }\n  tibble(sample = samples[i], gene = hit, type = type)\n})\n\nhead(mutations)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-822",
+      "lang": "r",
+      "code": "# Reshape the mutation table into a gene x sample matrix; a cell holds one or\n# several alteration types separated by \";\"\ngene_levels <- names(sort(table(factor(mutations$gene, levels = genes)), decreasing = TRUE))\nmat <- matrix(\"\", nrow = length(genes), ncol = length(samples),\n              dimnames = list(genes, samples))\nfor (i in seq_len(nrow(mutations))) {\n  cell <- mat[mutations$gene[i], mutations$sample[i]]\n  mat[mutations$gene[i], mutations$sample[i]] <-\n    if (cell == \"\") mutations$type[i] else paste(cell, mutations$type[i], sep = \";\")\n}\n\n# Order samples: by subtype, then by mutation count (waterfall look)\nmut_count <- colSums(mat != \"\")\nord <- order(factor(cohort, levels = c(\"Subtype A\", \"Subtype B\")), -mut_count)\nmat <- mat[gene_levels, ord]\n\n# Annotation vectors aligned with the reordered matrix\ncohort_ordered <- factor(cohort[ord], levels = c(\"Subtype A\", \"Subtype B\"))\ntmb <- mut_count[ord]\n\n# Colors for alteration types\nmutation_colors <- c(\n  Missense = \"#3690C0\", Nonsense = \"#A50F15\", Frameshift = \"#F16913\",\n  Splice_Site = \"#6A51A3\", In_Frame = \"#31A354\", Multi_Hit = \"#252525\"\n)\n\n# One drawing function per alteration type\nrect_fun <- function(color) {\n  function(x, y, w, h) grid.rect(x, y, w * 0.9, h * 0.9, gp = gpar(fill = color, col = NA))\n}\nalter_fun <- list(\n  background = rect_fun(\"#F2F2F2\"),\n  Missense = rect_fun(mutation_colors[\"Missense\"]),\n  Nonsense = rect_fun(mutation_colors[\"Nonsense\"]),\n  Frameshift = rect_fun(mutation_colors[\"Frameshift\"]),\n  Splice_Site = rect_fun(mutation_colors[\"Splice_Site\"]),\n  In_Frame = rect_fun(mutation_colors[\"In_Frame\"]),\n  Multi_Hit = rect_fun(mutation_colors[\"Multi_Hit\"])\n)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-822",
+      "lang": "r",
+      "code": "p1 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p1)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-822",
+      "lang": "r",
+      "code": "top_annotation <- HeatmapAnnotation(\n  TMB = anno_barplot(tmb, height = unit(1.1, \"cm\"),\n                     gp = gpar(fill = \"#6A51A3\", col = NA)),\n  annotation_name_gp = gpar(fontsize = 9))\n\np2 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  column_split = cohort_ordered, column_title_gp = gpar(fontsize = 10, fontface = \"bold\"),\n  top_annotation = top_annotation,\n  bottom_annotation = HeatmapAnnotation(\n    Subtype = as.character(cohort_ordered),\n    col = list(Subtype = c(\"Subtype A\" = \"#E08214\", \"Subtype B\" = \"#5E3C99\")),\n    annotation_name_side = \"left\", annotation_name_gp = gpar(fontsize = 9)),\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p2)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
+    },
+    {
+      "chartId": "MutationOncoplot-822",
+      "lang": "r",
+      "code": "pathway <- c(\n  TP53 = \"p53\", RB1 = \"p53\", CDKN2A = \"p53\",\n  EGFR = \"RTK/RAS\", ERBB2 = \"RTK/RAS\", MET = \"RTK/RAS\", KRAS = \"RTK/RAS\",\n  BRAF = \"RTK/RAS\", NF1 = \"RTK/RAS\",\n  PIK3CA = \"PI3K\", PTEN = \"PI3K\", STK11 = \"PI3K\", KEAP1 = \"PI3K\",\n  APC = \"WNT/Notch\", NOTCH1 = \"WNT/Notch\", FBXW7 = \"WNT/Notch\",\n  ARID1A = \"Chromatin\", SMAD4 = \"TGF-beta\", ATM = \"DDR\", BRCA2 = \"DDR\")\npathway_levels <- c(\"RTK/RAS\", \"PI3K\", \"p53\", \"WNT/Notch\", \"Chromatin\", \"TGF-beta\", \"DDR\")\n\np3 <- oncoPrint(mat,\n  alter_fun = alter_fun, alter_fun_is_vectorized = FALSE, col = mutation_colors,\n  column_order = samples[ord], show_column_names = FALSE,\n  row_split = factor(pathway[gene_levels], levels = pathway_levels),\n  row_title_gp = gpar(fontsize = 9, fontface = \"bold\"), row_title_rot = 0,\n  column_split = cohort_ordered, column_title_gp = gpar(fontsize = 10, fontface = \"bold\"),\n  top_annotation = top_annotation,\n  row_names_gp = gpar(fontsize = 9, fontface = \"italic\"), pct_gp = gpar(fontsize = 8),\n  heatmap_legend_param = list(title = \"Mutation type\"))\ndraw(p3)",
+      "packages": [
+        "ComplexHeatmap",
+        "tidyverse"
+      ],
+      "dataUrls": [],
+      "sourceAnchor": "https://openbiox.github.io/Bizard/Omics/MutationOncoplot.html"
     }
   ],
   "keywords": {
@@ -170370,8 +170779,8 @@
   },
   "citation": {
     "paperDoi": "10.1002/imm3.70038",
-    "paperUrl": "https://arxiv.org/abs/2503.06845",
-    "bibtex": "@article{wang2025bizard,\n  title={Bizard: an Open Atlas of Biomedical Data Visualization},\n  author={Wang, Shixiang and others},\n  journal={iMetaMed},\n  year={2025},\n  doi={10.1002/imm3.70038}\n}",
+    "paperUrl": "https://doi.org/10.1002/imm3.70038",
+    "bibtex": "@article{li2026bizard,\n  title={Bizard: A Community-Driven Platform for Accelerating and Enhancing Biomedical Data Visualization},\n  author={Li, Kexin and Zheng, Hu and Huang, Kexin and others},\n  journal={iMetaMed},\n  year={2026},\n  pages={e70038},\n  doi={10.1002/imm3.70038}\n}",
     "license": "CC-BY-NC-4.0"
   }
 }

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)
@@ -514,6 +514,11 @@
 - [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)
@@ -642,6 +647,11 @@
 - [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)
+
 ## 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)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openbiox/bizard-mcp",
-  "version": "0.1.2",
+  "version": "0.1.4",
   "description": "MCP server for the Bizard biomedical visualization atlas: search, adapt, cite, and contribute chart tutorials",
   "type": "module",
   "engines": { "node": ">=20" },