Plot the per base content as a heatmap

Plot the Per Base content for a set of FASTQC files.

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

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

# S4 method for class 'FastqcData'
plotSeqContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  bases = c("A", "T", "C", "G"),
  scaleColour = NULL,
  plotTheme = theme_get(),
  plotlyLegend = FALSE,
  expand.x = 0.02,
  expand.y = c(0, 0.05),
  ...
)

# S4 method for class 'FastqcDataList'
plotSeqContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  showPwf = TRUE,
  plotType = c("heatmap", "line", "residuals"),
  scaleColour = NULL,
  plotTheme = theme_get(),
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8,
  plotlyLegend = FALSE,
  nc = 2,
  ...
)

# S4 method for class 'FastpData'
plotSeqContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  module = c("Before_filtering", "After_filtering"),
  reads = c("read1", "read2"),
  readsBy = c("facet", "linetype"),
  moduleBy = c("facet", "linetype"),
  bases = c("A", "T", "C", "G", "N", "GC"),
  scaleColour = NULL,
  scaleLine = NULL,
  plotlyLegend = FALSE,
  plotTheme = theme_get(),
  expand.x = 0.02,
  expand.y = c(0, 0.05),
  ...
)

# S4 method for class 'FastpDataList'
plotSeqContent(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  module = c("Before_filtering", "After_filtering"),
  moduleBy = c("facet", "linetype"),
  reads = c("read1", "read2"),
  readsBy = c("facet", "linetype"),
  bases = c("A", "T", "C", "G", "N", "GC"),
  showPwf = FALSE,
  pwfCols,
  warn = 10,
  fail = 20,
  plotType = c("heatmap", "line", "residuals"),
  plotlyLegend = FALSE,
  scaleColour = NULL,
  scaleLine = NULL,
  plotTheme = theme_get(),
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8,
  expand.x = c(0.01),
  expand.y = c(0, 0.05),
  nc = 2,
  ...
)

Arguments

x

Can be a FastqcData, FastqcDataList or file paths

usePlotly

logical. Generate an interactive plot using plotly

labels

An optional named vector of labels for the file names. All file names must be present in the names of the vector.

pattern

Regex to remove from the end of any filenames

...

Used to pass additional attributes to plotting geoms

bases

Which bases to draw on the plot. Also becomes the default plotting order by setting these as factor levels

scaleColour

Discrete colour scale as a ggplot ScaleDiscrete object If not provided, will default to scale_colour_manual

plotTheme

theme object to be applied. Note that all plots will have theme_bw theme applied by default, as well as any additional themes supplied here

plotlyLegend

logical(1) Show legends for interactive plots. Ignored for heatmaps

expand.x, expand.y

Passed to expansion in the x- and y-axis scales respectively

pwfCols

Object of class PwfCols() to give colours for pass, warning, and fail values in plot

showPwf

Show PASS/WARN/FAIL categories as would be defined in a FastQC report

plotType

character. Type of plot to generate. Must be "line", "heatmap" or "residuals"

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

nc

Specify the number of columns if plotting a FastqcDataList as line plots. Passed to facet_wrap.

module

Fastp Module to show. Can only be Before/After_filtering

reads

Which set of reads to show

readsBy, moduleBy

When plotting both R1 & R2 and both modules, separate by either linetype or linetype

scaleLine

Discrete scale_linetype object. Only relevant if plotting values by linetype

warn, fail

Default values for WARN and FAIL based on FastQC reports. Only applied to heatmaps for FastpDataList objects

Value

A ggplot2 object or an interactive plotly object

Details

Per base sequence content (%A, %T, %G, %C), is shown as four overlaid heatmap colours when plotting from multiple reports. The individual line plots are able to be generated by setting plotType = "line", and the layout is determined by facet_wrap from ggplot2.

Individual line plots are also generated when plotting from a single FastqcData object.

If setting usePlotly = TRUE for a large number of reports, the plot can be slow to render. An alternative may be to produce a plot of residuals for each base, produced by taking the position-specific mean for each base.

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
plotSeqContent(fdl)


fp <- FastpData(system.file("extdata/fastp.json.gz", package = "ngsReports"))
plotSeqContent(fp)

plotSeqContent(fp, moduleBy = "linetype", bases = c("A", "C", "G", "T"))