Annotation

Click to expand the Neurons marker plots

Click to expand the Stromal marker plots

Click to expand the Astrocytes marker plots

Click to expand the Immune marker plots

Click to expand the Oligodendroglia marker plots

Click to expand the ependymal marker plots

## Warning in FetchData(object = object, vars = c(dims, "ident", features), : The
## following requested variables were not found: CD24A, MT2

Session information

Click to expand

## R version 4.0.4 (2021-02-15)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19041)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United Kingdom.1252 
## [2] LC_CTYPE=English_United Kingdom.1252   
## [3] LC_MONETARY=English_United Kingdom.1252
## [4] LC_NUMERIC=C                           
## [5] LC_TIME=English_United Kingdom.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] dplyr_1.0.5        ggsci_2.9          patchwork_1.1.1    ggplot2_3.3.3     
## [5] here_1.0.1         SeuratObject_4.0.0 Seurat_4.0.0      
## 
## loaded via a namespace (and not attached):
##   [1] Rtsne_0.15           colorspace_2.0-0     deldir_0.2-10       
##   [4] ellipsis_0.3.1       ggridges_0.5.3       rprojroot_2.0.2     
##   [7] spatstat.data_2.0-0  farver_2.1.0         leiden_0.3.7        
##  [10] listenv_0.8.0        ggrepel_0.9.1        fansi_0.4.2         
##  [13] codetools_0.2-18     splines_4.0.4        knitr_1.31          
##  [16] polyclip_1.10-0      jsonlite_1.7.2       ica_1.0-2           
##  [19] cluster_2.1.1        png_0.1-7            uwot_0.1.10         
##  [22] shiny_1.6.0          sctransform_0.3.2    compiler_4.0.4      
##  [25] httr_1.4.2           assertthat_0.2.1     Matrix_1.3-2        
##  [28] fastmap_1.1.0        lazyeval_0.2.2       later_1.1.0.1       
##  [31] htmltools_0.5.1.1    tools_4.0.4          igraph_1.2.6        
##  [34] gtable_0.3.0         glue_1.4.2           RANN_2.6.1          
##  [37] reshape2_1.4.4       Rcpp_1.0.6           spatstat_1.64-1     
##  [40] scattermore_0.7      jquerylib_0.1.3      vctrs_0.3.6         
##  [43] nlme_3.1-152         lmtest_0.9-38        xfun_0.21           
##  [46] stringr_1.4.0        globals_0.14.0       mime_0.10           
##  [49] miniUI_0.1.1.1       lifecycle_1.0.0      irlba_2.3.3         
##  [52] goftest_1.2-2        future_1.21.0        MASS_7.3-53.1       
##  [55] zoo_1.8-9            scales_1.1.1         promises_1.2.0.1    
##  [58] spatstat.utils_2.1-0 parallel_4.0.4       RColorBrewer_1.1-2  
##  [61] yaml_2.2.1           reticulate_1.18      pbapply_1.4-3       
##  [64] gridExtra_2.3        sass_0.3.1           rpart_4.1-15        
##  [67] stringi_1.5.3        highr_0.8            rlang_0.4.10        
##  [70] pkgconfig_2.0.3      matrixStats_0.58.0   evaluate_0.14       
##  [73] lattice_0.20-41      ROCR_1.0-11          purrr_0.3.4         
##  [76] tensor_1.5           htmlwidgets_1.5.3    labeling_0.4.2      
##  [79] cowplot_1.1.1        tidyselect_1.1.0     parallelly_1.24.0   
##  [82] RcppAnnoy_0.0.18     plyr_1.8.6           magrittr_2.0.1      
##  [85] R6_2.5.0             generics_0.1.0       DBI_1.1.1           
##  [88] pillar_1.5.1         withr_2.4.1          mgcv_1.8-34         
##  [91] fitdistrplus_1.1-3   survival_3.2-10      abind_1.4-5         
##  [94] tibble_3.1.0         future.apply_1.7.0   crayon_1.4.1        
##  [97] KernSmooth_2.23-18   utf8_1.2.1           plotly_4.9.3        
## [100] rmarkdown_2.7        grid_4.0.4           data.table_1.14.0   
## [103] digest_0.6.27        xtable_1.8-4         tidyr_1.1.3         
## [106] httpuv_1.5.5         munsell_0.5.0        viridisLite_0.3.0   
## [109] bslib_0.2.4

Annotation

Nadine Bestard

09/02/2021

Set-up

General Cluster

Annotation

Rename the Clusters with assigned Cell Types

Plot Cell type markers

Violin plot

Heat map

Session information