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knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) library(BiocStyle)
rm(list=ls()) library(devtools) devtools::install_github('zff-excellent/scImmuneGraph')
suppressMessages(library(scImmuneGraph))
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)
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)
data(tcontig_list) data(bcontig_list)
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)
# 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)
sessionInfo()
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