qc_plot_collection: Plot FastQC Results of multiple samples

View source: R/qc_plot_collection.R

qc_plot_collectionR Documentation

Plot FastQC Results of multiple samples


Plot FastQC data of multiple samples


qc_plot_collection(qc, modules = "all")



An object of class qc_read_collection or a path to the sample zipped fastqc result files.


Character vector containing the names of fastqc modules for which you want to import the data. Default is all. Allowed values include one or the combination of:

  • "Summary",

  • "Basic Statistics",

  • "Per base sequence quality",

  • "Per sequence quality scores",

  • "Per base sequence content",

  • "Per sequence GC content",

  • "Per base N content",

  • "Sequence Length Distribution",

  • "Sequence Duplication Levels",

  • "Overrepresented sequences",

  • "Adapter Content",

  • "Kmer Content"

Partial match of module names allowed. For example, you can use modules = "GC content", instead of the full names modules = "Per sequence GC content".


Returns a list of ggplots containing the plot for specified modules..


Mahmoud Ahmed, mahmoud.s.fahmy@students.kasralainy.edu.eg


qc.dir <- system.file("fastqc_results", package = "fastqcr")
qc.files <- list.files(qc.dir, full.names = TRUE)[1:2]
nb_samples <- length(qc.files)

# read specific modules in all files
# To read all modules, specify: modules = "all"
modules <- c(
  "Per sequence GC content",
  "Per base sequence quality",
 "Per sequence quality scores"
qc <- qc_read_collection(qc.files, sample_names = paste('S', 1:nb_samples, sep = ''),
       modules = modules)

# Plot per sequence GC content
qc_plot_collection(qc, "Per sequence GC content")

# Per base sequence quality
qc_plot_collection(qc, "Per base sequence quality")

# Per sequence quality scores
qc_plot_collection(qc, "Per sequence quality scores")

fastqcr documentation built on March 7, 2023, 8:16 p.m.