plotNContent-methods: Draw an N Content Plot

In ngsReports: Load FastqQC reports and other NGS related files

Description

Draw an N Content Plot across one or more FastQC reports

Usage

plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...)

## S4 method for signature 'ANY'
plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...)

## S4 method for signature 'character'
plotNContent(x, usePlotly = FALSE, labels, pwfCols, warn = 5, fail = 20, ...)

## S4 method for signature 'FastqcData'
plotNContent(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  warn = 5,
  fail = 20,
  ...,
  lineCol = "red"
)

## S4 method for signature 'FastqcDataList'
plotNContent(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  warn = 5,
  fail = 20,
  cluster = FALSE,
  dendrogram = FALSE,
  ...
)

Arguments

x	Can be a FastqcData, FastqcDataList or 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. File extensions are dropped by default
pwfCols	Object of class PwfCols containing the colours for PASS/WARN/FAIL
warn, fail	The default values for warn and fail are 5 and 10 respectively (i.e. percentages)
...	Used to pass additional attributes to theme() and between methods
lineCol	Defaults to red
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.

Details

This extracts the N_Content 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 FastqcData object line plots will always be drawn for all Ns. Otherwise, users can select line plots or heatmaps.

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
plotNContent(fdl[[1]])

ngsReports documentation built on Nov. 23, 2020, 2:01 a.m.