plotSummary-methods: Plot the PASS/WARN/FAIL information

In ngsReports: Load FastqQC reports and other NGS related files

Description

Extract the PASS/WARN/FAIL summaries and plot them

Usage

plotSummary(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  cluster = FALSE,
  dendrogram = FALSE,
  ...
)

## S4 method for signature 'ANY'
plotSummary(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  cluster = FALSE,
  dendrogram = FALSE,
  ...
)

## S4 method for signature 'character'
plotSummary(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  cluster = FALSE,
  dendrogram = FALSE,
  ...
)

## S4 method for signature 'FastqcDataList'
plotSummary(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  cluster = FALSE,
  dendrogram = FALSE,
  ...,
  gridlineWidth = 0.2,
  gridlineCol = "grey20"
)

Arguments

x	Can be a FastqcData, FastqcDataList or character vector of file paths
usePlotly	logical. Generate an interactive plot using plotly
labels	An optional named vector of labels for the file names. All filenames must be present in the names. File extensions are dropped by default.
pwfCols	Object of class PwfCols containing the colours for PASS/WARN/FAIL
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.
...	Used to pass various potting parameters to theme.
gridlineWidth, gridlineCol	Passed to geom_hline and geom_vline to determine width and colour of gridlines

Details

This uses the standard ggplot2 syntax to create a three colour plot. The output of this function can be further modified using the standard ggplot2 methods if required.

Value

A ggplot2 object (usePlotly = FALSE) or an interactive plotly object (usePlotly = TRUE)

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)

# Check the overall PASS/WARN/FAIL status
plotSummary(fdl)

ngsReports documentation built on Nov. 23, 2020, 2:01 a.m.