Pallial direct neurogenesis Fig.S1

Load libraries and QCFiltered dataset

# load libraries
library(Seurat)
library(RColorBrewer)

# Set ggplot theme
theme_set(theme_classic())

# Load the full annotated dataset
Allcells.data <- readRDS("./Clustered.cells.RDS")

Plot the different features

FeaturePlot(object = Allcells.data,
            features.plot = "BP_signature1",
            cols.use = rev(brewer.pal(10,"Spectral")),
            reduction.use = "spring",
            no.legend = T,
            overlay = F,
            dark.theme = F
            )

FeaturePlot(object = Allcells.data,
            features.plot = c("Top2a", "Eomes", "Mki67", "Btg2", "Cdk1", "Neurog2", "Aurka"),
            cols.use = c("grey90", brewer.pal(9,"YlGnBu")),
            reduction.use = "spring",
            no.legend = T,
            overlay = F,
            dark.theme = F)

Session Info

#date
format(Sys.time(), "%d %B, %Y, %H,%M")

## [1] "30 novembre, 2020, 11,35"

#Packages used
sessionInfo()

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
## LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
## 
## locale:
##  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] RColorBrewer_1.1-2 Seurat_2.3.4       Matrix_1.2-17      cowplot_1.0.0     
## [5] ggplot2_3.2.1     
## 
## loaded via a namespace (and not attached):
##   [1] Rtsne_0.15          colorspace_1.4-1    class_7.3-17       
##   [4] modeltools_0.2-22   ggridges_0.5.1      mclust_5.4.5       
##   [7] htmlTable_1.13.2    base64enc_0.1-3     rstudioapi_0.11    
##  [10] proxy_0.4-23        farver_2.0.1        npsurv_0.4-0       
##  [13] flexmix_2.3-15      bit64_4.0.2         codetools_0.2-16   
##  [16] splines_3.6.3       R.methodsS3_1.7.1   lsei_1.2-0         
##  [19] robustbase_0.93-5   knitr_1.26          zeallot_0.1.0      
##  [22] jsonlite_1.7.0      Formula_1.2-3       ica_1.0-2          
##  [25] cluster_2.1.0       kernlab_0.9-29      png_0.1-7          
##  [28] R.oo_1.23.0         compiler_3.6.3      httr_1.4.1         
##  [31] backports_1.1.5     assertthat_0.2.1    lazyeval_0.2.2     
##  [34] lars_1.2            acepack_1.4.1       htmltools_0.5.0    
##  [37] tools_3.6.3         igraph_1.2.5        gtable_0.3.0       
##  [40] glue_1.4.1          RANN_2.6.1          reshape2_1.4.3     
##  [43] dplyr_0.8.3         Rcpp_1.0.5          vctrs_0.2.0        
##  [46] gdata_2.18.0        ape_5.3             nlme_3.1-141       
##  [49] iterators_1.0.12    fpc_2.2-3           gbRd_0.4-11        
##  [52] lmtest_0.9-37       xfun_0.18           stringr_1.4.0      
##  [55] lifecycle_0.1.0     irlba_2.3.3         gtools_3.8.1       
##  [58] DEoptimR_1.0-8      MASS_7.3-53         zoo_1.8-6          
##  [61] scales_1.1.0        doSNOW_1.0.18       parallel_3.6.3     
##  [64] yaml_2.2.1          reticulate_1.13     pbapply_1.4-2      
##  [67] gridExtra_2.3       rpart_4.1-15        segmented_1.0-0    
##  [70] latticeExtra_0.6-28 stringi_1.4.6       foreach_1.4.7      
##  [73] checkmate_1.9.4     caTools_1.17.1.2    bibtex_0.4.2       
##  [76] Rdpack_0.11-0       SDMTools_1.1-221.1  rlang_0.4.7        
##  [79] pkgconfig_2.0.3     dtw_1.21-3          prabclus_2.3-1     
##  [82] bitops_1.0-6        evaluate_0.14       lattice_0.20-41    
##  [85] ROCR_1.0-7          purrr_0.3.3         labeling_0.3       
##  [88] htmlwidgets_1.5.1   bit_4.0.4           tidyselect_0.2.5   
##  [91] plyr_1.8.4          magrittr_1.5        R6_2.4.1           
##  [94] snow_0.4-3          gplots_3.0.1.1      Hmisc_4.3-0        
##  [97] pillar_1.4.2        foreign_0.8-72      withr_2.1.2        
## [100] fitdistrplus_1.0-14 mixtools_1.1.0      survival_2.44-1.1  
## [103] nnet_7.3-14         tsne_0.1-3          tibble_2.1.3       
## [106] crayon_1.3.4        hdf5r_1.3.2.9000    KernSmooth_2.23-15 
## [109] rmarkdown_2.5       grid_3.6.3          data.table_1.12.6  
## [112] metap_1.1           digest_0.6.25       diptest_0.75-7     
## [115] tidyr_1.0.0         R.utils_2.9.0       stats4_3.6.3       
## [118] munsell_0.5.0

---

1. Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, 75014, Paris, France, matthieu.moreau@inserm.fr↩