## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", message = FALSE, warning = FALSE ) ## ----loadPackage, echo = FALSE------------------------------------------------ require(utils) require(VDJdive) ## ----installation, eval = FALSE----------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("VDJdive") ## ----eval = FALSE------------------------------------------------------------- # # Read in a single file # contigs <- readVDJcontigs("path_to_10X_files") # # # Read in files for multiple samples # path1 <- "sample1" # path2 <- "sample2" # contigs <- readVDJcontigs(c("path1", "path2")) ## ----echo = FALSE------------------------------------------------------------- data("contigs") ## ----------------------------------------------------------------------------- require(SingleCellExperiment) ncells <- 24 u <- matrix(rpois(1000 * ncells, 5), ncol = ncells) barcodes <- vapply(contigs[,'barcode'], function(x){ x[1] }, 'A') samples <- vapply(contigs[,'sample'], function(x){ x[1] }, 'A') sce <- SingleCellExperiment(assays = list(counts = u), colData = data.frame(Barcode = barcodes, group = samples)) sce <- addVDJtoSCE(contigs, sce) sce$contigs ## ----------------------------------------------------------------------------- UNstats <- clonoStats(contigs, method = 'unique') class(UNstats) ## ----------------------------------------------------------------------------- EMstats <- clonoStats(contigs, method = "EM") class(EMstats) ## ----------------------------------------------------------------------------- sce <- clonoStats(sce, method = 'EM') metadata(sce) ## ----------------------------------------------------------------------------- head(clonoAbundance(sce)) # access output of abundance for clonotypes for clonoStats class clonoFrequency(sce) # access output of frequency for clonotypes for clonoStats class clonoFrequency(sce) # access output of clonotypes assignment for clonoStats class clonoGroup(sce) # access output of clonotypes grouping for clonoStats class clonoNames(sce) # access output of clonotypes samples for clonoStats class ## ----------------------------------------------------------------------------- div <- calculateDiversity(EMstats, methods = "all") div ## ----------------------------------------------------------------------------- #divBreakaway <- runBreakaway(EMstats, methods = 'unique') #divBreakaway ## ----------------------------------------------------------------------------- EMstats <- clonoStats(contigs, method = "EM", assignment = TRUE) clus <- sample(1:2, 24, replace = TRUE) EMstats.clus <- clonoStats(EMstats, group = clus) ## ----fig.width= 3, fig.height= 2---------------------------------------------- barVDJ(EMstats, title = "contigs", legend = TRUE) ## ----fig.width= 2.5, fig.height= 2-------------------------------------------- pieVDJ(EMstats) ## ----------------------------------------------------------------------------- sampleGroups <- data.frame(Sample = c("sample1", "sample2"), Group = c("Tumor", "Normal")) scatterVDJ(div, sampleGroups = NULL, title = "Evenness-abundance plot", legend = TRUE) ## ----------------------------------------------------------------------------- abundanceVDJ(EMstats) ## ----------------------------------------------------------------------------- sessionInfo()