1 Low and high cell number simulated from a E17.5 neural cortex dataset (Drop-seq) and hippocampus P0 dataset (10X)

mycolours <- c(
  "DSQ_H_4000_average"= "#E64B35FF" ,
  "DSQ_H_800_average" = "#4DBBD5FF" ,
  "DSQ_M_4000_average" = "#F39B7FFF"  ,
    "DSQ_M_800_average" = "#00A087FF",
  "10X_M_800_average" =  "#3C5488FF" ,
    "10X_M_4000_average"= "#8491B4FF" , 
  "DSQ_H_4000_sqrt"  = "#E64B35B2" ,
  "DSQ_H_800_sqrt"    ="#4DBBD5B2" ,
  "DSQ_M_4000_sqrt"   = "#F39B7FB2"  ,
  "DSQ_M_800_sqrt"    = "#00A087B2" ,
  "10X_M_800_sqrt"    = "#3C5488B2" ,
  "10X_M_4000_sqrt" = "#8491B4B2" 
  
  
  )

dodge <- position_dodge(width = 0.8)
  
si = 12
 nu= ggplot(nu.tot.plot,aes(x=cells, y=log(est)-log(nu), fill=group)) +
    facet_grid(method ~ ., scales = "free")+ 
    #ylim(-0.2,0.2)+
    geom_violin(color="black", position = dodge)+  
    facet_wrap(method ~ cells, scales = "free")+
    coord_flip()+
    scale_fill_manual(values =  mycolours)+
    xlab(TeX(" $log \\tilde{\\nu} - log \\nu $ "))+ geom_boxplot(width=0.3, outlier.colour=NA, position = dodge) +
    theme(axis.text.x = element_text(size = si, angle = 0, hjust = .5, vjust = .5, face = "plain", colour ="#3C5488FF" ),
        axis.text.y = element_text( size = si, angle = 0, hjust = 1, vjust = .0, face = "plain", colour ="#3C5488FF"),  
        axis.title.x = element_text( size = si, angle = 0, hjust = .5, vjust = 0, face = "plain", colour ="#3C5488FF"),
        axis.title.y = element_text( size = si, angle = 0, hjust = .5, vjust = .5, face = "plain", colour ="#3C5488FF"),
        legend.title = element_blank(),
       strip.background = element_rect(fill="#8491B44C"),
       strip.text.x = element_text(size = 12,colour = "#3C5488FF",face = "plain"),
        strip.text.y = element_text(size = 12,colour = "#3C5488FF",face = "plain"),
       axis.title.y.left = element_blank(),
       #legend.key.height = unit(5, "mm"),
        legend.text = element_text(color = "#3C5488FF",face ="italic" ),
        legend.position = "none")  # titl)

nu

Percentage of a < 0 :

sessionInfo()
#> R version 4.0.4 (2021-02-15)
#> 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/openblas/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] ggplot2_3.3.3      data.table_1.14.0  latex2exp_0.5.0    matrixStats_0.58.0
#> [5] stringr_1.4.0      scales_1.1.1       COTAN_0.1.0       
#> 
#> loaded via a namespace (and not attached):
#>  [1] sass_0.3.1           tidyr_1.1.2          jsonlite_1.7.2      
#>  [4] R.utils_2.10.1       bslib_0.2.4          assertthat_0.2.1    
#>  [7] highr_0.8            stats4_4.0.4         yaml_2.2.1          
#> [10] ggrepel_0.9.1        pillar_1.5.1         lattice_0.20-41     
#> [13] glue_1.4.2           reticulate_1.18      digest_0.6.27       
#> [16] RColorBrewer_1.1-2   colorspace_2.0-0     htmltools_0.5.1.1   
#> [19] Matrix_1.3-2         R.oo_1.24.0          pkgconfig_2.0.3     
#> [22] GetoptLong_1.0.5     purrr_0.3.4          tibble_3.1.0        
#> [25] generics_0.1.0       farver_2.1.0         IRanges_2.24.1      
#> [28] ellipsis_0.3.1       withr_2.4.1          BiocGenerics_0.36.0 
#> [31] magrittr_2.0.1       crayon_1.4.0         evaluate_0.14       
#> [34] R.methodsS3_1.8.1    fansi_0.4.2          Cairo_1.5-12.2      
#> [37] tools_4.0.4          GlobalOptions_0.1.2  formatR_1.8         
#> [40] lifecycle_1.0.0      ComplexHeatmap_2.6.2 basilisk.utils_1.2.2
#> [43] S4Vectors_0.28.1     munsell_0.5.0        cluster_2.1.1       
#> [46] compiler_4.0.4       jquerylib_0.1.3      rlang_0.4.10        
#> [49] grid_4.0.4           rjson_0.2.20         rappdirs_0.3.3      
#> [52] circlize_0.4.12      labeling_0.4.2       rmarkdown_2.7       
#> [55] basilisk_1.2.1       gtable_0.3.0         DBI_1.1.1           
#> [58] R6_2.5.0             knitr_1.31           dplyr_1.0.4         
#> [61] utf8_1.2.1           clue_0.3-58          filelock_1.0.2      
#> [64] shape_1.4.5          stringi_1.5.3        parallel_4.0.4      
#> [67] Rcpp_1.0.6           vctrs_0.3.6          png_0.1-7           
#> [70] tidyselect_1.1.0     xfun_0.22