Boxplot for each sample

Xiaotao Shen (https://www.shenxt.info/)

Created on 2021-12-04 and updated on 2022-09-19

Source: vignettes/massqc_sample_boxplot.Rmd

Data preparation 

library(massdataset)
library(tidyverse)
library(massqc)
data("sample_info", package = "massdataset")
data("expression_data", package = "massdataset")
data("variable_info", package = "massdataset")
object =
  create_mass_dataset(
    expression_data = expression_data,
    sample_info = sample_info,
    variable_info = variable_info
  )
object
#> -------------------- 
#> massdataset version: 0.99.1 
#> -------------------- 
#> 1.expression_data:[ 1000 x 8 data.frame]
#> 2.sample_info:[ 8 x 4 data.frame]
#> 3.variable_info:[ 1000 x 3 data.frame]
#> 4.sample_info_note:[ 4 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2022-01-16 22:54:57

Sample boxplot 


 object %>%
   log(10) %>%
   massqc_sample_boxplot(color_by = "class")


 object %>%
   log(10) %>%
   massqc_sample_boxplot(fill_by = "class") +
   ggsci::scale_fill_lancet()


 object %>%
   log(10) %>%
   massqc_sample_boxplot(
     fill_by = "class",
     color_by = "class",
     point = TRUE,
     point_alpha = 0.3
   ) +
   ggsci::scale_fill_lancet()


 object %>%
   log(10) %>%
   massqc_sample_boxplot(color_by = "class",
                  point = TRUE,
                  point_alpha = 0.3) +
   ggsci::scale_color_lancet()

Session information 

sessionInfo()
#> R Under development (unstable) (2022-01-11 r81473)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur/Monterey 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] ggfortify_0.4.14   massqc_0.0.1       forcats_0.5.1      stringr_1.4.0     
#>  [5] dplyr_1.0.7        purrr_0.3.4        readr_2.1.1        tidyr_1.1.4       
#>  [9] tibble_3.1.6       ggplot2_3.3.5      tidyverse_1.3.1    magrittr_2.0.1    
#> [13] tinytools_0.9.1    massdataset_0.99.1
#> 
#> loaded via a namespace (and not attached):
#>   [1] colorspace_2.0-2      rjson_0.2.21          ellipsis_0.3.2       
#>   [4] leaflet_2.0.4.1       rprojroot_2.0.2       circlize_0.4.14      
#>   [7] GlobalOptions_0.1.2   fs_1.5.2              clue_0.3-60          
#>  [10] rstudioapi_0.13       farver_2.1.0          ggrepel_0.9.1        
#>  [13] fansi_1.0.0           lubridate_1.8.0       xml2_1.3.3           
#>  [16] codetools_0.2-18      doParallel_1.0.16     cachem_1.0.6         
#>  [19] knitr_1.37            jsonlite_1.7.2        broom_0.7.11         
#>  [22] cluster_2.1.2         dbplyr_2.1.1          png_0.1-7            
#>  [25] compiler_4.2.0        httr_1.4.2            backports_1.4.1      
#>  [28] ggcorrplot_0.1.3      assertthat_0.2.1      fastmap_1.1.0        
#>  [31] lazyeval_0.2.2        cli_3.1.0             htmltools_0.5.2      
#>  [34] tools_4.2.0           gtable_0.3.0          glue_1.6.0           
#>  [37] Rcpp_1.0.7            Biobase_2.55.0        cellranger_1.1.0     
#>  [40] jquerylib_0.1.4       pkgdown_2.0.1         vctrs_0.3.8          
#>  [43] iterators_1.0.13      crosstalk_1.2.0       xfun_0.29            
#>  [46] openxlsx_4.2.5        rvest_1.0.2           lifecycle_1.0.1      
#>  [49] scales_1.1.1          ragg_1.2.1            clisymbols_1.2.0     
#>  [52] hms_1.1.1             parallel_4.2.0        RColorBrewer_1.1-2   
#>  [55] ComplexHeatmap_2.11.0 yaml_2.2.1            memoise_2.0.1        
#>  [58] pbapply_1.5-0         gridExtra_2.3         pander_0.6.4         
#>  [61] yulab.utils_0.0.4     sass_0.4.0            stringi_1.7.6        
#>  [64] highr_0.9             S4Vectors_0.33.10     desc_1.4.0           
#>  [67] foreach_1.5.1         BiocGenerics_0.41.2   zip_2.2.0            
#>  [70] shape_1.4.6           rlang_0.4.12          pkgconfig_2.0.3      
#>  [73] systemfonts_1.0.3     matrixStats_0.61.0    evaluate_0.14        
#>  [76] labeling_0.4.2        patchwork_1.1.1       htmlwidgets_1.5.4    
#>  [79] tidyselect_1.1.1      ggsci_2.9             plyr_1.8.6           
#>  [82] R6_2.5.1              IRanges_2.29.1        generics_0.1.1       
#>  [85] DBI_1.1.2             pillar_1.6.4          haven_2.4.3          
#>  [88] withr_2.4.3           modelr_0.1.8          crayon_1.4.2         
#>  [91] utf8_1.2.2            plotly_4.10.0         tzdb_0.2.0           
#>  [94] rmarkdown_2.11        GetoptLong_1.0.5      grid_4.2.0           
#>  [97] readxl_1.3.1          data.table_1.14.2     reprex_2.0.1         
#> [100] digest_0.6.29         gridGraphics_0.5-1    textshaping_0.3.6    
#> [103] stats4_4.2.0          munsell_0.5.0         viridisLite_0.4.0    
#> [106] ggplotify_0.1.0       bslib_0.3.1