Plot Overrepresented Kmers

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

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

# S4 method for class '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 class '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 class '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

Value

A standard ggplot2 object or an interactive plotly 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.

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")
)