完善优化《Seurat常用函数清单》

docs/quarto_foundation/quarto_shiny.html

@@ -598,7 +598,7 @@
 <p>本节我们介绍第三种方法，即在Quarto文档中通过<a href="https://posit-dev.github.io/r-shinylive/index.html#setup---quarto"><strong>quarto-shinylive extension</strong></a>嵌入Shiny应用程序。</p>
 <section id="安装shinylive包" class="level2" data-number="35.1"><h2 data-number="35.1" class="anchored" data-anchor-id="安装shinylive包">
 <span class="header-section-number">35.1</span> 安装<code>shinylive</code>包</h2>
-<p>要首先Shiny应用程序的嵌入，需要依赖<code>shinylive</code>包，可以从CRAN直接安装该包：</p>
+<p>要实现Shiny应用程序的嵌入，需要依赖<code>shinylive</code>包，可以从CRAN直接安装该包：</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode md code-with-copy"><code class="sourceCode markdown"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>install.packages("shinylive")</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section><section id="建立quarto-project" class="level2" data-number="35.2"><h2 data-number="35.2" class="anchored" data-anchor-id="建立quarto-project">
 <span class="header-section-number">35.2</span> 建立Quarto Project</h2>
@@ -1496,7 +1496,7 @@
 <span id="cb11-34"><a href="#cb11-34" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb11-35"><a href="#cb11-35" aria-hidden="true" tabindex="-1"></a><span class="fu">## 安装`shinylive`包</span></span>
 <span id="cb11-36"><a href="#cb11-36" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb11-37"><a href="#cb11-37" aria-hidden="true" tabindex="-1"></a>要首先Shiny应用程序的嵌入，需要依赖<span class="in">`shinylive`</span>包，可以从CRAN直接安装该包：</span>
+<span id="cb11-37"><a href="#cb11-37" aria-hidden="true" tabindex="-1"></a>要实现Shiny应用程序的嵌入，需要依赖<span class="in">`shinylive`</span>包，可以从CRAN直接安装该包：</span>
 <span id="cb11-38"><a href="#cb11-38" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb11-39"><a href="#cb11-39" aria-hidden="true" tabindex="-1"></a><span class="in">``` md</span></span>
 <span id="cb11-40"><a href="#cb11-40" aria-hidden="true" tabindex="-1"></a>install.packages("shinylive")</span>

docs/single_cell/seurat/data_visualization_methods_in_seurat.html

@@ -539,9 +539,7 @@
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block default"><div class="quarto-title">
-<div class="quarto-title-block"><div><h1 class="title">
-<span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Seurat中的数据可视化方法</span>
-</h1><button type="button" class="btn code-tools-button" id="quarto-code-tools-source"><i class="bi"></i> Code</button></div></div>
+<div class="quarto-title-block"><div><h1 class="title"><span id="sec-Data_visualization_methods_in_Seurat" class="quarto-section-identifier"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Seurat中的数据可视化方法</span></span></h1><button type="button" class="btn code-tools-button" id="quarto-code-tools-source"><i class="bi"></i> Code</button></div></div>
 </div>
 
 
@@ -772,7 +770,7 @@
 <div class="cell-output cell-output-stdout">
 <pre><code>R version 4.3.2 (2023-10-31)
 Platform: aarch64-apple-darwin20 (64-bit)
-Running under: macOS Sonoma 14.1.1
+Running under: macOS Sonoma 14.2.1
 
 Matrix products: default
 BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
@@ -788,45 +786,45 @@
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] ggplot2_3.4.4      Seurat_5.0.1       SeuratObject_5.0.1 sp_2.1-1          
+[1] ggplot2_3.4.4      Seurat_5.0.1       SeuratObject_5.0.1 sp_2.1-2          
 
 loaded via a namespace (and not attached):
   [1] deldir_2.0-2           pbapply_1.7-2          gridExtra_2.3         
   [4] rlang_1.1.2            magrittr_2.0.3         RcppAnnoy_0.0.21      
-  [7] spatstat.geom_3.2-7    matrixStats_1.1.0      ggridges_0.5.4        
- [10] compiler_4.3.2         png_0.1-8              vctrs_0.6.4           
+  [7] spatstat.geom_3.2-7    matrixStats_1.2.0      ggridges_0.5.5        
+ [10] compiler_4.3.2         png_0.1-8              vctrs_0.6.5           
  [13] reshape2_1.4.4         stringr_1.5.1          pkgconfig_2.0.3       
  [16] fastmap_1.1.1          ellipsis_0.3.2         labeling_0.4.3        
  [19] utf8_1.2.4             promises_1.2.1         rmarkdown_2.25        
- [22] purrr_1.0.2            xfun_0.41              jsonlite_1.8.7        
- [25] goftest_1.2-3          later_1.3.1            spatstat.utils_3.0-4  
- [28] irlba_2.3.5.1          parallel_4.3.2         cluster_2.1.4         
- [31] R6_2.5.1               ica_1.0-3              stringi_1.8.2         
+ [22] purrr_1.0.2            xfun_0.41              jsonlite_1.8.8        
+ [25] goftest_1.2-3          later_1.3.2            spatstat.utils_3.0-4  
+ [28] irlba_2.3.5.1          parallel_4.3.2         cluster_2.1.6         
+ [31] R6_2.5.1               ica_1.0-3              stringi_1.8.3         
  [34] RColorBrewer_1.1-3     spatstat.data_3.0-3    reticulate_1.34.0     
  [37] parallelly_1.36.0      lmtest_0.9-40          scattermore_1.2       
  [40] Rcpp_1.0.11            knitr_1.45             tensor_1.5            
  [43] future.apply_1.11.0    zoo_1.8-12             sctransform_0.4.1     
- [46] httpuv_1.6.12          Matrix_1.6-3           splines_4.3.2         
- [49] igraph_1.5.1           tidyselect_1.2.0       abind_1.4-5           
- [52] rstudioapi_0.15.0      yaml_2.3.7             spatstat.random_3.2-1 
+ [46] httpuv_1.6.13          Matrix_1.6-4           splines_4.3.2         
+ [49] igraph_1.6.0           tidyselect_1.2.0       abind_1.4-5           
+ [52] rstudioapi_0.15.0      yaml_2.3.8             spatstat.random_3.2-2 
  [55] codetools_0.2-19       miniUI_0.1.1.1         spatstat.explore_3.2-5
  [58] listenv_0.9.0          lattice_0.22-5         tibble_3.2.1          
  [61] plyr_1.8.9             withr_2.5.2            shiny_1.8.0           
- [64] ROCR_1.0-11            evaluate_0.23          Rtsne_0.16            
+ [64] ROCR_1.0-11            evaluate_0.23          Rtsne_0.17            
  [67] future_1.33.0          fastDummies_1.7.3      survival_3.5-7        
  [70] polyclip_1.10-6        fitdistrplus_1.1-11    pillar_1.9.0          
  [73] KernSmooth_2.23-22     plotly_4.10.3          generics_0.1.3        
- [76] RcppHNSW_0.5.0         munsell_0.5.0          scales_1.2.1          
+ [76] RcppHNSW_0.5.0         munsell_0.5.0          scales_1.3.0          
  [79] globals_0.16.2         xtable_1.8-4           glue_1.6.2            
- [82] lazyeval_0.2.2         tools_4.3.2            data.table_1.14.8     
+ [82] lazyeval_0.2.2         tools_4.3.2            data.table_1.14.10    
  [85] RSpectra_0.16-1        RANN_2.6.1             leiden_0.4.3.1        
- [88] dotCall64_1.1-0        cowplot_1.1.1          grid_4.3.2            
- [91] tidyr_1.3.0            colorspace_2.1-0       nlme_3.1-163          
- [94] patchwork_1.1.3        cli_3.6.1              spatstat.sparse_3.0-3 
- [97] spam_2.10-0            fansi_1.0.5            viridisLite_0.4.2     
+ [88] dotCall64_1.1-1        cowplot_1.1.2          grid_4.3.2            
+ [91] tidyr_1.3.0            colorspace_2.1-0       nlme_3.1-164          
+ [94] patchwork_1.1.3        cli_3.6.2              spatstat.sparse_3.0-3 
+ [97] spam_2.10-0            fansi_1.0.6            viridisLite_0.4.2     
 [100] dplyr_1.1.4            uwot_0.1.16            gtable_0.3.4          
 [103] digest_0.6.33          progressr_0.14.0       ggrepel_0.9.4         
-[106] farver_2.1.1           htmlwidgets_1.6.3      htmltools_0.5.7       
+[106] farver_2.1.1           htmlwidgets_1.6.4      htmltools_0.5.7       
 [109] lifecycle_1.0.4        httr_1.4.7             mime_0.12             
 [112] MASS_7.3-60           </code></pre>
 </div>
@@ -1262,7 +1260,7 @@
       </a>
   </div>
 </nav><div class="modal fade" id="quarto-embedded-source-code-modal" tabindex="-1" aria-labelledby="quarto-embedded-source-code-modal-label" aria-hidden="true"><div class="modal-dialog modal-dialog-scrollable"><div class="modal-content"><div class="modal-header"><h5 class="modal-title" id="quarto-embedded-source-code-modal-label">Source Code</h5><button class="btn-close" data-bs-dismiss="modal"></button></div><div class="modal-body"><div class="">
-<div class="sourceCode" id="cb27" data-shortcodes="false"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="fu"># Seurat中的数据可视化方法</span></span>
+<div class="sourceCode" id="cb27" data-shortcodes="false"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="fu"># Seurat中的数据可视化方法 {#sec-Data_visualization_methods_in_Seurat}</span></span>
 <span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a><span class="at">&gt; 原文：</span><span class="co">[</span><span class="ot">*Data visualization methods in Seurat*</span><span class="co">](https://satijalab.org/seurat/articles/visualization_vignette)</span></span>
 <span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a><span class="at">&gt;</span></span>