qc_plot: Plot FastQC Results

Description Usage Arguments Value Examples

View source: R/qc_plot.R

Description

Plot FastQC data

Usage

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qc_plot(qc, modules = "all")

## S3 method for class 'qctable'
print(x, ...)

Arguments

qc

An object of class qc_read or a path to the sample zipped fastqc result file.

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".

x

an object of class qctable.

...

other arguments.

Value

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

Examples

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# Demo file
qc.file <- system.file("fastqc_results", "S1_fastqc.zip",  package = "fastqcr")
qc.file
# Read all modules
qc <- qc_read(qc.file)

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

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

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

# Per base sequence content
qc_plot(qc, "Per base sequence content")

# Sequence duplication levels
qc_plot(qc, "Sequence duplication levels")

fastqcr documentation built on May 2, 2019, 2:13 a.m.