Draw an N Content Plot — plotNContent • ngsReports

Draw an N Content Plot across one or more FastQC reports

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

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

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

# S4 method for class '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 class '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 class '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

Value

A standard ggplot2 object, or an interactive plotly object

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.

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)
  )
)