plotBaseQuals-methods: Plot the Base Qualities for each file

In steveped/ngsReports: Load FastqQC reports and other NGS related files

Plot the Base Qualities for each file

Description

Plot the Base Qualities for each file as separate plots

Usage

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

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

## S4 method for signature 'FastqcData'
plotBaseQuals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 25,
  fail = 20,
  boxWidth = 0.8,
  showPwf = TRUE,
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastqcDataList'
plotBaseQuals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 25,
  fail = 20,
  showPwf = TRUE,
  boxWidth = 0.8,
  plotType = c("heatmap", "boxplot"),
  plotValue = "Mean",
  cluster = FALSE,
  dendrogram = FALSE,
  nc = 2,
  heat_w = 8L,
  ...
)

## S4 method for signature 'FastpData'
plotBaseQuals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 25,
  fail = 20,
  showPwf = FALSE,
  module = c("Before_filtering", "After_filtering"),
  reads = c("read1", "read2"),
  readsBy = c("facet", "linetype"),
  bases = c("A", "T", "C", "G", "mean"),
  scaleColour = NULL,
  plotTheme = theme_get(),
  plotlyLegend = FALSE,
  ...
)

## S4 method for signature 'FastpDataList'
plotBaseQuals(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  pwfCols,
  warn = 25,
  fail = 20,
  showPwf = FALSE,
  module = c("Before_filtering", "After_filtering"),
  plotType = "heatmap",
  plotValue = c("mean", "A", "T", "C", "G"),
  scaleFill = NULL,
  plotTheme = theme_get(),
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8L,
  ...
)

Arguments

x	Can be a FastqcData, FastqcDataList or character vector of 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 remove from the end of the Fastp report and Fastq file names
...	Used to pass additional attributes to theme() and between methods
pwfCols	Object of class PwfCols() to give colours for pass, warning, and fail values in plot
warn, fail	The default values for warn and fail are 30 and 20 respectively (i.e. percentages)
boxWidth	set the width of boxes when using a boxplot
showPwf	Include the Pwf status colours
plotlyLegend	logical(1) Show legend for interactive plots. Only called when drawing line plots
plotType	character Can be either "boxplot" or "heatmap"
plotValue	character Type of data to be presented. Can be any of the columns returned by the appropriate call to getModule()
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.
nc	numeric. The number of columns to create in the plot layout. Only used if drawing boxplots for multiple files in a FastqcDataList
heat_w	Relative width of any heatmap plot components
module	Select Before and After filtering when using a FastpDataList
reads	Create plots for read1, read2 or all when using a FastpDataList
readsBy	If paired reads are present, separate using either linetype or by facet
bases	Which bases to include on the plot
scaleColour	ggplot discrete colour scale, passed to lines
plotTheme	theme object
scaleFill	ggplot2 continuous scale. Passed to heatmap cells

Details

When acting on a FastqcDataList, this defaults to a heatmap using the mean Per_base_sequence_quality score. A set of plots which replicate those obtained through a standard FastQC html report can be obtained by setting plotType = "boxplot", which uses facet_wrap to provide the layout as a single ggplot object.

When acting an a FastqcData object, this replicates the ⁠Per base sequence quality⁠ plots from FastQC with no faceting.

For large datasets, subsetting by R1 or R2 reads may be helpful.

An interactive plot can be obtained by setting usePlotly = TRUE.

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)

# The default plot for multiple libraries is a heatmap
plotBaseQuals(fdl)

# The default plot for a single library is the standard boxplot
plotBaseQuals(fdl[[1]])

# FastpData objects have qyalities by base
fp <-  FastpData(system.file("extdata/fastp.json.gz", package = "ngsReports"))
plotBaseQuals(
  fp, plotTheme = theme(plot.title = element_text(hjust = 0.5))
)

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