Draw a PCA plot for Fast QC modules

Draw a PCA plot for Fast QC modules across multiple samples

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

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

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

# S4 method for class '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

Value

A standard ggplot2 object, or an interactive plotly object

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()

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)
#> Too few points to calculate an ellipse
#> Too few points to calculate an ellipse
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_path()`).