Last updated: 2021-05-04

Checks: 7 0

Knit directory: STUtility_web_site/

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Ignored files:
    Ignored:    .DS_Store
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Manual_annotation.Rmd) and HTML (docs/Manual_annotation.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd fc3278a Ludvig Larsson 2021-05-04 Updated website with new theme and content
html 9fe84d9 Ludvig Larsson 2021-05-04 Build site.
html bfe87d1 Ludvig Larsson 2021-05-04 Build site.
Rmd eba61ce Ludvig Larsson 2021-05-04 Updated website with new theme and content
html 1dc000c Ludvig Larsson 2021-04-28 Build site.
html 1e9c615 Ludvig Larsson 2021-04-28 Build site.
html 34884bd Ludvig Larsson 2020-10-06 Build site.
html d13dabd Ludvig Larsson 2020-06-05 Build site.
html 60407bb Ludvig Larsson 2020-06-05 Build site.
html e339ebc Ludvig Larsson 2020-06-05 Build site.
html 6606127 Ludvig Larsson 2020-06-05 Build site.
html f0ea9c1 Ludvig Larsson 2020-06-05 Build site.
html 651f315 Ludvig Larsson 2020-06-05 Build site.
Rmd 09fb881 Ludvig Larsson 2020-06-04 wflow_git_commit(all = T)
html 09fb881 Ludvig Larsson 2020-06-04 wflow_git_commit(all = T)
html fb06450 jbergenstrahle 2020-01-11 Build site.
Rmd baff98e jbergenstrahle 2019-12-16 adding
Rmd 5cb8ab1 jbergenstrahle 2019-12-02 update2

Included in STutility is a Shiny application for manual annotation. It lets the user select and give a/several specific capture-spot(s) a label. This could be used for e.g. visualization or DEA purposes. Instructions for how to use the tool is included in the actual app. By default, the app will open in browser mode. When the annotation is completed, simply close the browser window and return to R.

#NOTE: Following the usual workflow of Seurat, we save the output from the function to our object

se <- ManualAnnotation(se)
 

A work by Joseph Bergenstråhle and Ludvig Larsson

 


sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] STutility_0.1.0 ggplot2_3.3.3   Seurat_3.1.5    workflowr_1.6.2

loaded via a namespace (and not attached):
  [1] uuid_0.1-4              backports_1.1.6         systemfonts_0.2.1      
  [4] plyr_1.8.6              igraph_1.2.6            lazyeval_0.2.2         
  [7] sp_1.4-1                splines_4.0.5           crosstalk_1.1.1        
 [10] listenv_0.8.0           digest_0.6.27           foreach_1.5.0          
 [13] htmltools_0.5.1.1       viridis_0.5.1           magick_2.3             
 [16] tiff_0.1-5              gdata_2.18.0            fansi_0.4.2            
 [19] magrittr_2.0.1          cluster_2.1.1           doParallel_1.0.15      
 [22] ROCR_1.0-11             globals_0.14.0          gmodels_2.18.1         
 [25] jpeg_0.1-8.1            colorspace_2.0-0        blob_1.2.1             
 [28] ggrepel_0.9.1           xfun_0.13               dplyr_1.0.5            
 [31] crayon_1.4.1            jsonlite_1.7.2          zeallot_0.1.0          
 [34] survival_3.2-10         zoo_1.8-9               iterators_1.0.12       
 [37] ape_5.4-1               glue_1.4.2              gtable_0.3.0           
 [40] webshot_0.5.2           leiden_0.3.7            future.apply_1.7.0     
 [43] scales_1.1.1            DBI_1.1.0               miniUI_0.1.1.1         
 [46] Rcpp_1.0.6              viridisLite_0.3.0       xtable_1.8-4           
 [49] spData_0.3.5            units_0.6-6             reticulate_1.18        
 [52] spdep_1.1-3             rsvd_1.0.3              akima_0.6-2            
 [55] tsne_0.1-3              htmlwidgets_1.5.3       httr_1.4.2             
 [58] RColorBrewer_1.1-2      ellipsis_0.3.1          ica_1.0-2              
 [61] pkgconfig_2.0.3         uwot_0.1.10             deldir_0.1-25          
 [64] utf8_1.2.1              tidyselect_1.1.0        rlang_0.4.10           
 [67] manipulateWidget_0.10.1 reshape2_1.4.4          later_1.1.0.1          
 [70] munsell_0.5.0           tools_4.0.5             dbscan_1.1-5           
 [73] generics_0.1.0          ggridges_0.5.3          evaluate_0.14          
 [76] stringr_1.4.0           fastmap_1.0.1           yaml_2.2.1             
 [79] knitr_1.28              fs_1.5.0                fitdistrplus_1.1-3     
 [82] rgl_0.100.54            purrr_0.3.4             RANN_2.6.1             
 [85] readbitmap_0.1.5        pbapply_1.4-3           future_1.21.0          
 [88] nlme_3.1-152            whisker_0.4             mime_0.10              
 [91] ggiraph_0.7.7           compiler_4.0.5          plotly_4.9.3           
 [94] png_0.1-7               e1071_1.7-3             Morpho_2.8             
 [97] tibble_3.1.0            stringi_1.5.3           gdtools_0.2.2          
[100] lattice_0.20-41         Matrix_1.3-2            classInt_0.4-3         
[103] shinyjs_1.1             vctrs_0.3.7             LearnBayes_2.15.1      
[106] pillar_1.5.1            lifecycle_1.0.0         lmtest_0.9-38          
[109] RcppAnnoy_0.0.18        data.table_1.14.0       cowplot_1.1.1          
[112] irlba_2.3.3             Rvcg_0.19.1             raster_3.1-5           
[115] httpuv_1.5.2            patchwork_1.1.1         colorRamps_2.3         
[118] R6_2.5.0                imager_0.42.1           promises_1.2.0.1       
[121] KernSmooth_2.23-18      gridExtra_2.3           bmp_0.3                
[124] parallelly_1.24.0       codetools_0.2-18        gtools_3.8.2           
[127] boot_1.3-27             MASS_7.3-53.1           assertthat_0.2.1       
[130] rprojroot_1.3-2         withr_2.4.1             sctransform_0.2.1      
[133] expm_0.999-4            parallel_4.0.5          grid_4.0.5             
[136] tidyr_1.1.3             coda_0.19-3             class_7.3-18           
[139] rmarkdown_2.1           Rtsne_0.15              git2r_0.27.1           
[142] sf_0.9-7                shiny_1.4.0.2