plotNContent-methods: Draw an N Content Plot

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

Draw an N Content Plot

Description

Draw an N Content Plot across one or more FastQC reports

Usage

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

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

## S4 method for signature 'FastqcData'
plotNContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 5,
  fail = 20,
  showPwf = TRUE,
  ...,
  lineCol = "red"
)

## S4 method for signature 'FastqcDataList'
plotNContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 5,
  fail = 20,
  showPwf = TRUE,
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8,
  scaleFill = NULL,
  ...
)

## S4 method for signature 'FastpData'
plotNContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  module = c("Before_filtering", "After_filtering"),
  moduleBy = c("facet", "colour", "linetype"),
  reads = c("read1", "read2"),
  readsBy = c("facet", "colour", "linetype"),
  scaleColour = NULL,
  scaleLine = NULL,
  plotTheme = theme_get(),
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastpDataList'
plotNContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  module = c("Before_filtering", "After_filtering"),
  reads = c("read1", "read2"),
  scaleFill = NULL,
  plotTheme = theme_get(),
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8,
  ...
)

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.
pattern	Regex used to trim the end of filenames
...	Used to pass additional attributes to theme() for FastqcData objects and to geom* calls for FastpData-based objects
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)
showPwf	logical(1) Show the PASS/WARN/FAIL status
lineCol	Line colours
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	Relative width of any heatmap plot components
scaleFill, scaleColour, scaleLine	ggplot2 scale objects
module	Used for Fastp* structures to show results before or after filtering
moduleBy, readsBy	How to show each module or set of reads on the plot
reads	Show plots for read1, read2 or both.
plotTheme	theme object
plotlyLegend	logical(1) Show legend on interactive plots

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

## Using a Fastp Data object
fl <- system.file("extdata/fastp.json.gz", package = "ngsReports")
fp <- FastpData(fl)
plotNContent(fp)
plotNContent(
  fp, pattern = "_001.+",
  moduleBy = "colour", scaleColour = scale_colour_brewer(palette = "Set1"),
  plotTheme = theme(
    legend.position = 'inside', legend.position.inside = c(0.99, 0.99),
    legend.justification = c(1, 1), plot.title = element_text(hjust = 0.5)
  )
)

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