Draw an Adapter Content Plot

Draw an Adapter Content Plot across one or more FASTQC reports

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

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

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

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

# S4 method for class '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

Value

A standard ggplot2 object, or an interactive plotly object

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

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"))