Draw a barplot of read totals

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

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

# S4 method for class 'FastqcDataList'
plotReadTotals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  duplicated = TRUE,
  bars = c("stacked", "adjacent"),
  vertBars = TRUE,
  divBy = 1,
  barCols = c("red", "blue"),
  expand.y = c(0, 0.02),
  plotlyLegend = FALSE,
  ...
)

# S4 method for class 'FastpDataList'
plotReadTotals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  adjPaired = TRUE,
  divBy = 1e+06,
  scaleFill = NULL,
  labMin = 0.05,
  status = TRUE,
  labelVJ = 0.5,
  labelFill = "white",
  plotTheme = theme_get(),
  vertBars = FALSE,
  plotlyLegend = FALSE,
  expand.y = c(0, 0.05),
  ...
)

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 used to trim the end of filenames
...: Used to pass additional attributes to theme()
duplicated: logical(1). Include deduplicated read total estimates to plot charts
bars: If duplicated = TRUE, show unique and deduplicated reads as "stacked" or "adjacent".
vertBars: logical(1) Show bars as vertical or horizontal
divBy: Scale read totals by this value. The default shows the y-axis in millions for FastpDataList objects, but does not scale FastQC objects, for the sake of backwards compatability
barCols: Colours for duplicated and unique reads.
expand.y: Passed to ggplot2::expansion for the axis showing totals
plotlyLegend: logical(1) Show legend on interactive plots
adjPaired: Scale read totals by 0.5 when paired
scaleFill: ScaleDiscrete function to be applied to the plot
labMin: Only show labels for filtering categories higher than this values as a proportion of reads. Set to any number > 1 to turn off labels
status: logical(1) Include read status in the plot
labelVJ: Relative vertical position to labels within each bar.
labelFill: Passed to geom_label
plotTheme: theme to be added to the plot

Value

Returns a ggplot or plotly object

Details

Draw a barplot of read totals using the standard ggplot2 syntax. The raw data from readTotals() can otherwise be used to manually create a plot.

Duplication levels are based on the value shown on FASTQC reports at the top of the DeDuplicatedTotals plot, which is known to be inaccurate. As it still gives a good guide as to sequence diversity it is included as the default. This can be turned off by setting duplicated = FALSE.

For FastpDataList objects, duplication statistics are not part of the default module containing ReadTotals. However, the status of reads and the reason for being retained or filtered is, and as such these are shown instead of duplication statistics.

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)

# Plot the Read Totals showing estimated duplicates
plotReadTotals(fdl)


# Plot the Read Totals without estimated duplicates
plotReadTotals(fdl, duplicated = FALSE)