plotAdapterContent-methods: Draw an Adapter Content Plot

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

Draw an Adapter Content Plot

Description

Draw an Adapter Content Plot across one or more FASTQC reports

Usage

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

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

## S4 method for signature 'FastqcData'
plotAdapterContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  showPwf = TRUE,
  warn = 5,
  fail = 10,
  scaleColour = NULL,
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastqcDataList'
plotAdapterContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  showPwf = TRUE,
  warn = 5,
  fail = 10,
  plotType = c("heatmap", "line"),
  adapterType = "Total",
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8L,
  scaleFill = NULL,
  scaleColour = NULL,
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastpData'
plotAdapterContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  scaleFill = NULL,
  plotlyLegend = FALSE,
  plotTheme = theme_get(),
  ...
)

## S4 method for signature 'FastpDataList'
plotAdapterContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  showPwf = FALSE,
  warn = 5,
  fail = 10,
  cluster = FALSE,
  dendrogram = FALSE,
  scaleFill = NULL,
  plotTheme = theme_get(),
  heat_w = 8L,
  ...
)

Arguments

x	Can be a FastqcData, a FastqcDataList or character vector of file paths
usePlotly	logical. Output as ggplot2 (default) or plotly object.
labels	An optional named vector of labels for the file names. All filenames must be present in the names.
pattern	regex used to trim the ends of all filenames for plotting
...	Used to pass additional attributes to theme() for FastQC objects and geoms for Fastp objects
pwfCols	Object of class PwfCols() containing the colours for PASS/WARN/FAIL
showPwf	logical(1) Show PASS/WARN/FAIL status as would be included in a standard FastQC report
warn, fail	The default values for warn and fail are 5 and 10 respectively (i.e. percentages)
plotlyLegend	logical(1) Show legend when choosing interactive plots. Ignored for heatmaps
plotType	character. Can only take the values plotType = "heatmap" or plotType = "line"
adapterType	A regular expression matching the adapter(s) to be plotted. To plot all adapters summed, specify adapterType = "Total". This is the default behaviour.
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.
heat_w	Width of the heatmap relative to other plot components
scaleFill, scaleColour	scale_fill\* and scale_colour_\* objects
plotTheme	Set theme elements by passing a theme

Details

This extracts the Adapter_Content module from the supplied object and generates a ggplot2 object, with a set of minimal defaults. The output of this function can be further modified using the standard ggplot2 methods.

When x is a single or FastqcData object line plots will always be drawn for all adapters. Otherwise, users can select line plots or heatmaps. When plotting more than one fastqc file, any undetected adapters will not be shown.

An interactive version of the plot can be made by setting usePlotly as TRUE

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)

# The default plot
plotAdapterContent(fdl)

# Also subset the reads to just the R1 files
r1 <- grepl("R1", fqName(fdl))
plotAdapterContent(fdl[r1])

# Plot just the Universal Adapter
# and change the y-axis using ggplot2::scale_y_continuous
plotAdapterContent(fdl, adapterType ="Illumina_Universal", plotType = "line") +
facet_wrap(~Filename) +
guides(colour = "none")

# For FastpData object, the plots are slightly different
fp <- FastpData(system.file("extdata/fastp.json.gz", package = "ngsReports"))
plotAdapterContent(fp, scaleFill = scale_fill_brewer(palette = "Set1"))

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