plotSeqContent-methods: Plot the per base content as a heatmap

In steveped/ngsReports: Load FastqQC reports and other NGS related files

Plot the per base content as a heatmap

Description

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

Usage

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

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

## S4 method for signature '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 signature '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 signature '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 signature '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

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.

Value

A 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
plotSeqContent(fdl)

fp <- FastpData(system.file("extdata/fastp.json.gz", package = "ngsReports"))
plotSeqContent(fp)
plotSeqContent(fp, moduleBy = "linetype", bases = c("A", "C", "G", "T"))

steveped/ngsReports documentation built on July 24, 2024, 10:45 a.m.