plotReadTotals-methods: Draw a barplot of read totals

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

Draw a barplot of read totals

Description

Draw a barplot of read totals

Usage

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

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

## S4 method for signature '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 signature '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

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.

Value

Returns a ggplot or 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)

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

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

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