SeuratExplorerServer

Q: 为什么搞这个R包
A: SeuratExplorer相当于一个桌面版软件，可以在本地电脑上查看和分析Seurat对象，即使把SeuratExplorer安装到服务器上，那也只能通过上传数据来浏览客户端电脑上的Seurat对象，无法查看位于服务器上的数据。SeuratExplorerServer的开发目的是，允许用户利用服务器硬件资源，通过网页浏览器来查看位于服务器上的Seurat对象数据，该R包不仅具有SeuratExplorerR 包的所有功能外，还可以查看中间分析结果，并且支持多数据切换、密码保护功能和自定义部分初始化参数。

Q: 为啥要多数据切换
A:有时在做完分析后，会需要提取某些cell type的细胞，然后再重新分析，得到新的Seurat对象，这样同一个project下就会有多个Seurat对象。

Q: 为什么需要密码保护
A:对于未公开的数据，一般会仅仅允许数据相关的人员可以获取和查看数据。对于已发表的数据，可以选择不设置密码。

Q: SeuratExplorer与SeuratExplorerServer的关系
A:SeuratExplorerServer依赖于SeuratExplorer，并且具备所有SeuratExplorer里的功能。

Q: SeuratExplorerServer支持的分析报告类型
A: pdf, html, tiff, csv, jpg, jpeg, png, bmp, svg等，也可以通过修改functions.R里的prepare_reportsfunction，来指定其它类型的文件。

1. Installation

You can install the development version of SeuratExplorer and SeuratExplorerServerlike so:

if(!require(devtools)){install.packages("devtools")}
install_github("fentouxungui/SeuratExplorer")
options(timeout = max(300, getOption("timeout")))
install_github("fentouxungui/SeuratExplorerServer")

2. Run a demo

library(SeuratExplorerServer)
launchSeuratExplorerServer()

launchSeuratExplorerServer Parameters:

Encrypted: whether to encrypt the App
credentials: You must specify this parameter when Encrypted is set to TRUE
paramterfile: see bellow for detailed information

3. Workflow introduction

首先在App所在目录（比如：Fly-Gut-EEs-scRNAseq）的上层目录创建同名的并以_reports为后缀的目录（Fly-Gut-EEs-scRNAseq_reports），sample meta中Reports.main列和Reports.second列对应目录中里的特定类型的文件，会以快捷连接方式被放到reports目录中。这会导致App加载延迟。
登录：输入账户和密码。
sample meta信息展示及下载。
选择或切换数据。
浏览分析报告。
SeuratExplorer里的功能。
修改样本元信息的默认参数，重启后生效。
关闭时会删除_reports目录（Fly-Gut-EEs-scRNAseq_reports）

4. Examples deployed on Shinyserver

A live demo.

# app.R
options(timeout = max(300, getOption("timeout")))

if(!require(devtools)){install.packages("devtools")}
if(!require(SeuratExplorer)){install_github("fentouxungui/SeuratExplorer")}
if(!require(SeuratExplorerServer)){install_github("fentouxungui/SeuratExplorerServer")}

Encrypted = TRUE
credentials = data.frame(user = "shiny", password = "12345", stringsAsFactors = FALSE)
paramterfile = SeuratExplorerServer:::revise_path()
TechnicianEmail = "zhangyongchao@nibs.ac.cn"
TechnicianName = "ZhangYongchao"

shinyApp(
  ui = SeuratExplorerServer::ui(Encrypted.app = Encrypted, TechnicianEmail = TechnicianEmail, TechnicianName = TechnicianName),
  server = SeuratExplorerServer::server, onStart = SeuratExplorerServer:::onStart(Encrypted, credentials, paramterfile)
)

5. Usage

5.1 Generate credentials

Please refer to R package shinymanager for detailed tutorial to generate a credentials data in data.frame.

# Init DB using credentials data
credentials <- data.frame(
  user = "shiny",
  password = "12345",
  stringsAsFactors = FALSE
)

5.2 Generate sample metadata parameters

data_meta <- data.frame(
  Reports.main = c("inst/extdata/demo/fly-gut-EEs-scRNA", "inst/extdata/demo/mouse-gut-haber"), # 主分析目录, Rds文件位于此目录中，并且所有位于该目录下的指定文件也会被收录到reports中，以sample name进行命名和区分。
  Rds.path = c("Rds-file/G101_PC20res04.rds", "haber.tsne.embeding.rds"), # Rds文件在主分析目录中的相对目录
  Reports.second = c(NA, NA), # 次要分析目录，此目录中的分析报告也会被加载到reports临时目录中，比如cellranger的结果。放到Others子目录下。
  Sample.name = c("Fly-Gut-EEs-scRNAseq-GuoXT", "Mouse-Intestine-scRNAseq-Haber"), # Sample name
  SplitOptions.MaxLevel = c(1, 4), # 用于设定split选项的参数,如果是多样本数据合并，一般该值要大于或等于样本数。
  Default.DimensionReduction = c("tsne", "umap"), # dimension reduction的默认值。
  Default.ClusterResolution = c("res.0.4", NA),  # cluster的默认值。
  Species = c("Fly", "Mouse"), # Human, Mouse, Fly or Others
  Description = c("blabla","hahaha"), # descript the sample or the analsyis, or whatever.
  stringsAsFactors = FALSE)
knitr::kable(data_meta)

Reports.main	Rds.path	Reports.second	Sample.name	SplitOptions.MaxLevel	Default.DimensionReduction	Default.ClusterResolution	Species	Description
inst/extdata/demo/fly-gut-EEs-scRNA	Rds-file/G101_PC20res04.rds	NA	Fly-Gut-EEs-scRNAseq-GuoXT	1	tsne	res.0.4	Fly	blabla
inst/extdata/demo/mouse-gut-haber	haber.tsne.embeding.rds	NA	Mouse-Intestine-scRNAseq-Haber	4	umap	NA	Mouse	hahaha

# saveRDS(data_meta, file = "sample-paramters.rds")

Or:

data_meta <- SeuratExplorerServer::initialize_metadata(
  Reports.main = c("inst/extdata/demo/fly-gut-EEs-scRNA", "inst/extdata/demo/mouse-gut-haber"), # 必填项目
  Rds.path = c("Rds-file/G101_PC20res04.rds", "haber.tsne.embeding.rds"), # 必填项目
  Reports.second = c(NA, NA), # 必填项目
  Sample.name = c("Fly-Gut-EEs-scRNAseq-GuoXT", "Mouse-Intestine-scRNAseq-Haber")) # 必填项目
#> data meta file check passed!
#> data meta file initilized successfully!

knitr::kable(data_meta)

Reports.main	Rds.path	Reports.second	Sample.name	Species	Description	Default.DimensionReduction	Default.ClusterResolution	SplitOptions.MaxLevel
inst/extdata/demo/fly-gut-EEs-scRNA	Rds-file/G101_PC20res04.rds	NA	Fly-Gut-EEs-scRNAseq-GuoXT	NA	NA	NA	NA	NA
inst/extdata/demo/mouse-gut-haber	haber.tsne.embeding.rds	NA	Mouse-Intestine-scRNAseq-Haber	NA	NA	NA	NA	NA

# saveRDS(data_meta, file = "sample-paramters.rds")

其他参数可以在App运行过程中进行修改。必填项目一般是由数据分析员设定的，其他参数可由用户自行设定。

5.3 Explore data

library(SeuratExplorerServer)
launchSeuratExplorerServer(Encrypted = TRUE, 
                           credentials = credentials,
                           paramterfile = "sample-paramters.rds",
                           TechnicianEmail = "your-email",
                           TechnicianName = "your-name")

6. Screenshots

7. To Do List

支持空间转录组数据，SeuratExplorer related，比较复杂，以后有精力再做.

8. Rsession info

#> R version 4.4.1 (2024-06-14 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 22631)
#> 
#> Matrix products: default
#> 
#> 
#> locale:
#> [1] LC_COLLATE=Chinese (Simplified)_China.utf8 
#> [2] LC_CTYPE=Chinese (Simplified)_China.utf8   
#> [3] LC_MONETARY=Chinese (Simplified)_China.utf8
#> [4] LC_NUMERIC=C                               
#> [5] LC_TIME=Chinese (Simplified)_China.utf8    
#> 
#> time zone: Asia/Shanghai
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>   [1] RColorBrewer_1.1-3              rstudioapi_0.16.0              
#>   [3] jsonlite_1.8.8                  billboarder_0.4.1              
#>   [5] magrittr_2.0.3                  spatstat.utils_3.0-5           
#>   [7] rmarkdown_2.27                  vctrs_0.6.5                    
#>   [9] ROCR_1.0-11                     memoise_2.0.1                  
#>  [11] spatstat.explore_3.2-7          askpass_1.2.0                  
#>  [13] htmltools_0.5.8.1               SeuratExplorerServer_0.0.1.0000
#>  [15] sass_0.4.9                      sctransform_0.4.1              
#>  [17] parallelly_1.37.1               KernSmooth_2.23-24             
#>  [19] bslib_0.7.0                     htmlwidgets_1.6.4              
#>  [21] ica_1.0-3                       plyr_1.8.9                     
#>  [23] plotly_4.10.4                   zoo_1.8-12                     
#>  [25] cachem_1.1.0                    igraph_2.0.3                   
#>  [27] mime_0.12                       lifecycle_1.0.4                
#>  [29] pkgconfig_2.0.3                 Matrix_1.7-0                   
#>  [31] R6_2.5.1                        fastmap_1.2.0                  
#>  [33] fitdistrplus_1.1-11             future_1.33.2                  
#>  [35] shiny_1.8.1.1                   digest_0.6.36                  
#>  [37] colorspace_2.1-0                patchwork_1.2.0                
#>  [39] Seurat_5.1.0                    tensor_1.5                     
#>  [41] RSpectra_0.16-1                 irlba_2.3.5.1                  
#>  [43] RSQLite_2.3.7                   progressr_0.14.0               
#>  [45] fansi_1.0.6                     spatstat.sparse_3.1-0          
#>  [47] httr_1.4.7                      polyclip_1.10-6                
#>  [49] abind_1.4-5                     compiler_4.4.1                 
#>  [51] bit64_4.0.5                     DBI_1.2.3                      
#>  [53] fastDummies_1.7.3               highr_0.11                     
#>  [55] R.utils_2.12.3                  MASS_7.3-60.2                  
#>  [57] openssl_2.2.0                   tools_4.4.1                    
#>  [59] lmtest_0.9-40                   httpuv_1.6.15                  
#>  [61] future.apply_1.11.2             goftest_1.2-3                  
#>  [63] R.oo_1.26.0                     glue_1.7.0                     
#>  [65] nlme_3.1-164                    promises_1.3.0                 
#>  [67] grid_4.4.1                      Rtsne_0.17                     
#>  [69] cluster_2.1.6                   reshape2_1.4.4                 
#>  [71] generics_0.1.3                  gtable_0.3.5                   
#>  [73] spatstat.data_3.1-2             R.methodsS3_1.8.2              
#>  [75] tidyr_1.3.1                     data.table_1.15.4              
#>  [77] sp_2.1-4                        utf8_1.2.4                     
#>  [79] spatstat.geom_3.2-9             RcppAnnoy_0.0.22               
#>  [81] ggrepel_0.9.5                   shinymanager_1.0.410           
#>  [83] RANN_2.6.1                      pillar_1.9.0                   
#>  [85] stringr_1.5.1                   spam_2.10-0                    
#>  [87] RcppHNSW_0.6.0                  later_1.3.2                    
#>  [89] splines_4.4.1                   dplyr_1.1.4                    
#>  [91] lattice_0.22-6                  bit_4.0.5                      
#>  [93] survival_3.6-4                  deldir_2.0-4                   
#>  [95] tidyselect_1.2.1                miniUI_0.1.1.1                 
#>  [97] pbapply_1.7-2                   knitr_1.47                     
#>  [99] gridExtra_2.3                   scattermore_1.2                
#> [101] xfun_0.45                       shinydashboard_0.7.2           
#> [103] matrixStats_1.3.0               DT_0.33                        
#> [105] stringi_1.8.4                   scrypt_0.1.6                   
#> [107] lazyeval_0.2.2                  yaml_2.3.8                     
#> [109] shinyWidgets_0.8.6              evaluate_0.24.0                
#> [111] codetools_0.2-20                tibble_3.2.1                   
#> [113] cli_3.6.3                       uwot_0.2.2                     
#> [115] xtable_1.8-4                    reticulate_1.38.0              
#> [117] munsell_0.5.1                   jquerylib_0.1.4                
#> [119] Rcpp_1.0.12                     SeuratExplorer_0.0.6.0000      
#> [121] globals_0.16.3                  spatstat.random_3.2-3          
#> [123] png_0.1-8                       parallel_4.4.1                 
#> [125] blob_1.2.4                      ggplot2_3.5.1                  
#> [127] dotCall64_1.1-1                 listenv_0.9.1                  
#> [129] viridisLite_0.4.2               scales_1.3.0                   
#> [131] ggridges_0.5.6                  SeuratObject_5.0.2             
#> [133] leiden_0.4.3.1                  purrr_1.0.2                    
#> [135] rlang_1.1.4                     cowplot_1.1.3

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README.md

README.md

SeuratExplorerServer

1. Installation

2. Run a demo

3. Workflow introduction

4. Examples deployed on Shinyserver

5. Usage

5.1 Generate credentials

5.2 Generate sample metadata parameters

5.3 Explore data

6. Screenshots

7. To Do List

8. Rsession info

Files

README.md

Latest commit

History

README.md

File metadata and controls

SeuratExplorerServer

1. Installation

2. Run a demo

3. Workflow introduction

4. Examples deployed on Shinyserver

5. Usage

5.1 Generate credentials

5.2 Generate sample metadata parameters

5.3 Explore data

6. Screenshots

7. To Do List

8. Rsession info