plotFastqcPCA-methods: Draw a PCA plot for Fast QC modules

In UofABioinformaticsHub/fastqcReports: Load FastqQC reports and other NGS related files

Draw a PCA plot for Fast QC modules

Description

Draw a PCA plot for Fast QC modules across multiple samples \lifecycleexperimental

Usage

plotFastqcPCA(
  x,
  module = "Per_sequence_GC_content",
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  sz = 4,
  groups,
  ...
)

## S4 method for signature 'ANY'
plotFastqcPCA(
  x,
  module = "Per_sequence_GC_content",
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  sz = 4,
  groups,
  ...
)

## S4 method for signature 'character'
plotFastqcPCA(
  x,
  module = "Per_sequence_GC_content",
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  sz = 4,
  groups,
  ...
)

## S4 method for signature 'FastqcDataList'
plotFastqcPCA(
  x,
  module = "Per_sequence_GC_content",
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  sz = 4,
  groups,
  pc = c(1, 2),
  ...
)

Arguments

x	Can be a FastqcDataList or character vector of file paths
module	character vector containing the desired FastQC module (eg. c("Per_base_sequence_quality", "Per_base_sequence_content"))
usePlotly	logical. Output as ggplot2 (default) or plotly object.
labels	An optional named vector of labels for the file names. All file names must be present in the names of the vector.
pattern	Regex to remove from the end of any filenames
sz	The size of the text labels
groups	Optional factor of the same length as x. If provided, the plot will be coloured using this factor as the defined groups. Ellipses will also be added to the final plot.
...	Used to pass additional attributes to theme() and between methods
pc	The two components to be plotted

Details

This carries out PCA on a single FastQC module and plots the output using either ggplot or plotly. Current modules for PCA are Per_base_sequence_quality, Per_sequence_quality_scores, Per_sequence_GC_content, Per_base_sequence_content, and Sequence_Length_Distribution.

If a factor is provided in the groups argument, this will be applied to the plotting colours and ellipses will be drawn using these groups. Only the labels will be plotted using geom_text()

Value

A standard ggplot2 object, or an interactive plotly object

Examples

# Get the files included with the package
packageDir <- system.file("extdata", package = "ngsReports")
fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE)

# Load the FASTQC data as a FastqcDataList object
fdl <- FastqcDataList(fl)
grp <- as.factor(gsub(".+(R[12]).*", "\\1", fqName(fdl)))
plotFastqcPCA(fdl, module = "Per_sequence_GC_content", groups = grp)

UofABioinformaticsHub/fastqcReports documentation built on July 23, 2024, 3:26 p.m.