Plot FastQC Results of multiple samples

Source: R/qc_plot_collection.R

Plot FastQC data of multiple samples

qc_plot_collection(qc, modules = "all")

Arguments

qc

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

modules

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".

Value

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

Examples

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)
#> Reading: /private/var/folders/xm/8p6yj4bj6s57n4v_51714lwm0000gp/T/RtmpT6jSz8/temp_libpatha9b37e9f6eab/fastqcr/fastqc_results/S1_fastqc.zip
#> Reading: /private/var/folders/xm/8p6yj4bj6s57n4v_51714lwm0000gp/T/RtmpT6jSz8/temp_libpatha9b37e9f6eab/fastqcr/fastqc_results/S2_fastqc.zip

# 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")