1 Installation Package

rm(list=ls())
library(devtools)
devtools::install_github('zff-excellent/scImmuneGraph')
suppressMessages(library(scImmuneGraph))

2 Converting 10X genomics produced B cell contigs file(s) as a list outputed

  • For TCR
project_data_dir <- "F:/R_Language/data/tcr"
sample_name <- list.dirs(project_data_dir, full.names = FALSE, recursive = FALSE)
group_name <- c("A", "A", "B", "B")

contig_list <- TCR.ContigList(project_data_dir, sample_name, group_name)
  • For BCR
project_data_dir <- "F:/R_Language/data/bcr"
sample_name <- list.dirs(project_data_dir, full.names = FALSE, recursive = FALSE)
group_name <- c("A", "A", "B", "B")

contig_list <- BCR.ContigList(project_data_dir, sample_name, group_name)

3 Getting Data

  • tcontig_list : TCR dataset from the 10x Genomics Chromium Immune Profiling.
  • bcontig_list : BCR dataset from the 10x Genomics Chromium Immune Profiling.
data(tcontig_list)
data(bcontig_list)

4 TCR basic information statistics

contig_list <- tcontig_list
sample_name <- names(contig_list)

multi_plots <- TCR.ClonalStateDistribution(contig_list, sample_name)
cowplot::plot_grid(plotlist=multi_plots)

# Or all functions as the same call way
multi_plots <- BasicPlot(TCR.ClonalStateDistribution, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(TCR.top100ClonotypeAbundance, contig_list, sample_name)
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(TCR.ClonotypeComposition, contig_list, sample_name) # Diversity 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(TCR.top100CDR3Abundance, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(TCR.CDR3ntLengthDistribution, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(TCR.VgeneAbundance, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(TCR.JgeneAbundance, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(TCR.VJgenePair, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

5 BCR basic information statistics

# contig_list <- BCR.ContigList(project_data_dir, sample_name, group_name)
contig_list <- bcontig_list
sample_name <- names(contig_list)
multi_plots <- BasicPlot(BCR.ClonalStateDistribution, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(BCR.top100ClonotypeAbundance, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(BCR.ClonotypeComposition, contig_list, sample_name) 
# cowplot::plot_grid(plotlist=multi_plots)
multi_plots <- BasicPlot(BCR.top100CDR3Abundance, contig_list, sample_name)
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(BCR.CDR3ntLengthDistribution, contig_list, sample_name)
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(BCR.VgeneAbundance, contig_list, sample_name)
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(BCR.JgeneAbundance, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

multi_plots <- BasicPlot(BCR.VJgenePair, contig_list, sample_name) 
cowplot::plot_grid(plotlist=multi_plots)

6 Session Info

sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17763)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=C                              
## [2] LC_CTYPE=Chinese (Simplified)_China.936   
## [3] LC_MONETARY=Chinese (Simplified)_China.936
## [4] LC_NUMERIC=C                              
## [5] LC_TIME=Chinese (Simplified)_China.936    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] scImmuneGraph_1.1.3 BiocStyle_2.18.1   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7          highr_0.9           bslib_0.3.1        
##  [4] compiler_4.0.2      pillar_1.6.4        RColorBrewer_1.1-2 
##  [7] BiocManager_1.30.16 jquerylib_0.1.4     forcats_0.5.1      
## [10] tools_4.0.2         digest_0.6.27       gtable_0.3.0       
## [13] jsonlite_1.7.2      evaluate_0.14       lifecycle_1.0.1    
## [16] tibble_3.1.5        pkgconfig_2.0.3     rlang_0.4.10       
## [19] DBI_1.1.1           magick_2.7.3        yaml_2.2.1         
## [22] xfun_0.23           fastmap_1.1.0       dplyr_1.0.7        
## [25] stringr_1.4.0       knitr_1.36          gtools_3.9.2       
## [28] generics_0.1.0      vctrs_0.3.8         sass_0.4.0         
## [31] cowplot_1.1.1       grid_4.0.2          tidyselect_1.1.1   
## [34] glue_1.4.2          R6_2.5.1            fansi_0.5.0        
## [37] rmarkdown_2.11      bookdown_0.24       farver_2.1.0       
## [40] tidyr_1.1.4         ggplot2_3.3.5       purrr_0.3.4        
## [43] magrittr_2.0.1      scales_1.1.1        htmltools_0.5.2    
## [46] ellipsis_0.3.2      assertthat_0.2.1    colorspace_2.0-2   
## [49] labeling_0.4.2      utf8_1.2.2          stringi_1.7.5      
## [52] munsell_0.5.0       crayon_1.4.1