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Plot Cell Barcode demultiplex statistics

Source: R/find_barcode.R
plot_demultiplex.Rd

produce a barplot of cell barcode demultiplex statistics

Usage

plot_demultiplex(find_barcode_result)

Arguments

find_barcode_result

output from find_barcode

Value

a list of ggplot objects:

  • reads_count_plot: stacked barplot of: demultiplexed reads

  • knee_plot: knee plot of UMI counts before TSO trimming

  • flank_editdistance_plot: flanking sequence (adaptor) edit-distance plot

  • barcode_editdistance_plot: barcode edit-distance plot

  • cutadapt_plot: if TSO trimming is performed, number of reads kept by cutadapt

Examples

outdir <- tempfile()
dir.create(outdir)
fastq_dir <- tempfile()
dir.create(fastq_dir)
file.copy(system.file("extdata", "fastq", "musc_rps24.fastq.gz", package = "FLAMES"),
  file.path(fastq_dir, "musc_rps24.fastq.gz"))
#> [1] TRUE
sampled_lines <- readLines(file.path(fastq_dir, "musc_rps24.fastq.gz"), n = 400)
writeLines(sampled_lines, file.path(fastq_dir, "copy.fastq"))
bc_allow <- file.path(outdir, "bc_allow.tsv")
R.utils::gunzip(
  filename = system.file("extdata", "bc_allow.tsv.gz", package = "FLAMES"),
  destname = bc_allow, remove = FALSE
)
find_barcode(
  fastq = fastq_dir,
  stats_out = file.path(outdir, "bc_stat"),
  reads_out = file.path(outdir, "demultiplexed.fq"),
  barcodes_file = bc_allow, TSO_seq = "CCCATGTACTCTGCGTTGATACCACTGCTT"
) |>
  plot_demultiplex()
#> FLEXIPLEX 0.96.2
#> Setting max barcode edit distance to 2
#> Setting max flanking sequence edit distance to 8
#> Setting read IDs to be  replaced
#> Setting number of threads to 1
#> Search pattern: 
#> primer: CTACACGACGCTCTTCCGATCT
#> BC: NNNNNNNNNNNNNNNN
#> UMI: NNNNNNNNNNNN
#> polyT: TTTTTTTTT
#> Setting known barcodes from /tmp/RtmpoS7Kzz/file1f6d66ad1306/bc_allow.tsv
#> Number of known barcodes: 143
#> Processing file: /tmp/RtmpoS7Kzz/file1f6d5bd6075c/copy.fastq
#> Searching for barcodes...
#> Processing file: /tmp/RtmpoS7Kzz/file1f6d5bd6075c/musc_rps24.fastq.gz
#> Searching for barcodes...
#> Number of reads processed: 493
#> Number of reads where at least one barcode was found: 460
#> Number of reads with exactly one barcode match: 455
#> Number of chimera reads: 2
#> All done!
#> $reads_count_plot

#> 
#> $knee_plot
#> `geom_smooth()` using formula = 'y ~ x'

#> 
#> $flank_editdistance_plot

#> 
#> $barcode_editdistance_plot
#> Warning: The following aesthetics were dropped during statistical transformation: fill.
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?

#> 
#> $cutadapt_plot

#>