plotOverrep-methods: Plot a summary of Over-represented Sequences
In steveped/ngsReports: Load FastqQC reports and other NGS related files

plotOverrep

R Documentation

Plot a summary of Over-represented Sequences

Description

Plot a summary of Over-represented Sequences for a set of FASTQC reports

Usage

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

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

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

## S4 method for signature 'FastqcData'
plotOverrep(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  n = 10,
  expand.x = c(0, 0, 0.05, 0),
  expand.y = c(0, 0.6, 0, 0.6),
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastqcDataList'
plotOverrep(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  showPwf = TRUE,
  cluster = FALSE,
  dendrogram = FALSE,
  scaleFill = NULL,
  paletteName = "Set1",
  panel_w = 8,
  expand.x = c(0, 0, 0.05, 0),
  expand.y = rep(0, 4),
  ...
)

Arguments

`x`	Can be a `FastqcData`, `FastqcDataList` or file paths
`usePlotly`	`logical` Default `FALSE` will render using ggplot. If `TRUE` plot will be rendered with plotly
`labels`	An optional named factor of labels for the file names. All filenames must be present in the names.
`pattern`	Regex to remove from the end of any filenames
`pwfCols`	Object of class `PwfCols()` containing the colours for PASS/WARN/FAIL
`...`	Used to pass additional attributes to theme() and between methods
`n`	The number of sequences to plot from an individual file
`expand.x`, `expand.y`	Output from `expansion()` or numeric vectors of length 4. Passed to `⁠scale_*_continuous()⁠`
`plotlyLegend`	Show legend on interactive plots
`showPwf`	Show PASS/WARN/FAIL status on the plot
`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.
`scaleFill`	ggplot scale object
`paletteName`	Name of the palette for colouring the possible sources of the overrepresented sequences. Must be a palette name from `RColorBrewer`. Ignored if specifying the scaleFill separately
`panel_w`	Width of main panel on output

Details

Percentages are obtained by simply summing those within a report. Any possible double counting by FastQC is ignored for the purposes of a simple approximation.

Plots generated from a FastqcData object will show the top n sequences grouped by their predicted source & coloured by whether the individual sequence would cause a WARN/FAIL.

Plots generated from a FastqcDataList group sequences by predicted source and summarise as a percentage of the total reads.

Value

A standard ggplot2 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)

# A brief summary across all FastQC reports
plotOverrep(fdl)

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