plotKmers-methods: Plot Overrepresented Kmers

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

Plot Overrepresented Kmers

Description

Plot Overrepresented Kmers

Usage

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

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

## S4 method for signature 'FastqcData'
plotKmers(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  n = 6,
  linewidth = 0.5,
  plotlyLegend = FALSE,
  scaleColour = NULL,
  pal = c("red", "blue", "green", "black", "magenta", "yellow"),
  ...
)

## S4 method for signature 'FastqcDataList'
plotKmers(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  cluster = FALSE,
  dendrogram = FALSE,
  pwfCols,
  showPwf = TRUE,
  scaleFill = NULL,
  heatCol = hcl.colors(50, "inferno"),
  heat_w = 8,
  ...
)

## S4 method for signature 'FastpData'
plotKmers(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  module = c("Before_filtering", "After_filtering"),
  reads = c("read1", "read2"),
  readsBy = c("facet", "mean", "diff"),
  trans = "log2",
  scaleFill = NULL,
  plotTheme = theme_get(),
  plotlyLegend = FALSE,
  ...
)

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 vector of labels for the file names. All filenames must be present in the names.
pattern	regex to drop from the end of filenames
...	Used to pass parameters to theme for FastqcData objects and to geoms for FastpData objects
n	numeric. The number of Kmers to show.
linewidth	Passed to geom_line()
plotlyLegend	Show legend for interactive plots
pal	The colour palette. If the vector supplied is less than n, grDevices::colorRampPalette() will be used
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.
pwfCols	Object of class PwfCols() to give colours for pass, warning, and fail values in the plot
showPwf	Show the PASS/WARN/FAIL status
scaleFill, scaleColour	ggplot2 scales to be used for colour palettes
heatCol	Colour palette used for the heatmap. Default is inferno from the viridis set of palettes
heat_w	Relative width of any heatmap plot components
module	The module to obtain data from when using a FastpData object
reads	Either read1 or read2. Only used when using a FastpData object
readsBy	Strategy for visualising both read1 and read2. Can be set to show each set of reads by facet, or within the same plot taking the mean of the enrichment above mean, or the difference in the enrichment above mean
trans	Function for transforming the count/mean ratio. Set as NULL to use the ratio without transformation
plotTheme	theme object

Details

As the Kmer Content module present in FastQC reports is relatively uninformative, and omitted by default in later versions of FastQC, these are rudimentary plots.

Plots for FastqcData objects replicate those contained in a FastQC report, whilst the heatmap generated from FastqcDataList objects simply show the location and abundance of over-represented Kmers.

Value

A standard 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)
plotKmers(fdl[[1]])

# Use a FastpData object
fl <- system.file("extdata", "fastp.json.gz", package = "ngsReports")
fp <- FastpData(fl)
plotKmers(fp, size = 2)
plotKmers(
  fp, reads = "read1", size = 2, trans = NULL,
  scaleFill = scale_fill_gradient(low = "white", high = "black")
)

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