plotOverrep-methods: Plot a summary of Over-represented Sequences

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

Plot a summary of Over-represented Sequences

Description

Plot a summary of Over-represented Sequences for a set of FASTQC reports

Usage

plotOverrep(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  ...
)

## S4 method for signature 'ANY'
plotOverrep(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  ...
)

## S4 method for signature 'character'
plotOverrep(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  ...
)

## S4 method for signature 'FastqcData'
plotOverrep(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  n = 10,
  expand.x = c(0, 0, 0.05, 0),
  expand.y = c(0, 0.6, 0, 0.6),
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastqcDataList'
plotOverrep(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  showPwf = TRUE,
  cluster = FALSE,
  dendrogram = FALSE,
  scaleFill = NULL,
  paletteName = "Set1",
  panel_w = 8,
  expand.x = c(0, 0, 0.05, 0),
  expand.y = rep(0, 4),
  ...
)

Arguments

x	Can be a FastqcData, FastqcDataList or file paths
usePlotly	logical Default FALSE will render using ggplot. If TRUE plot will be rendered with plotly
labels	An optional named factor of labels for the file names. All filenames must be present in the names.
pattern	Regex to remove from the end of any filenames
pwfCols	Object of class PwfCols() containing the colours for PASS/WARN/FAIL
...	Used to pass additional attributes to theme() and between methods
n	The number of sequences to plot from an individual file
expand.x, expand.y	Output from expansion() or numeric vectors of length 4. Passed to ⁠scale_*_continuous()⁠
plotlyLegend	Show legend on interactive plots
showPwf	Show PASS/WARN/FAIL status on the plot
cluster	logical default FALSE. If set to TRUE, fastqc data will be clustered using hierarchical clustering
dendrogram	logical redundant if cluster is FALSE if both cluster and dendrogram are specified as TRUE then the dendrogram will be displayed.
scaleFill	ggplot scale object
paletteName	Name of the palette for colouring the possible sources of the overrepresented sequences. Must be a palette name from RColorBrewer. Ignored if specifying the scaleFill separately
panel_w	Width of main panel on output

Details

Percentages are obtained by simply summing those within a report. Any possible double counting by FastQC is ignored for the purposes of a simple approximation.

Plots generated from a FastqcData object will show the top n sequences grouped by their predicted source & coloured by whether the individual sequence would cause a WARN/FAIL.

Plots generated from a FastqcDataList group sequences by predicted source and summarise as a percentage of the total reads.

Value

A standard ggplot2 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)

# A brief summary across all FastQC reports
plotOverrep(fdl)

UofABioinformaticsHub/fastqcReports documentation built on April 1, 2024, 5:29 p.m.