Introduction to scImmuneGraph"

In scImmuneGraph: Visualize the Basic Characteristics of Single-Cell Immune Repertoire

knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)
library(BiocStyle)

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Installation Package

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

suppressMessages(library(scImmuneGraph))

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)

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)

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)

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)

Session Info

sessionInfo()

scImmuneGraph documentation built on Dec. 10, 2021, 5:11 p.m.