R: Plot the per base content as a heatmap

plotSeqContent {ngsReports}

R Documentation

Plot the per base content as a heatmap

Description

Plot the Per Base content for a set of FASTQC files.

Usage

plotSeqContent(x, usePlotly = FALSE, labels, ...)

## S4 method for signature 'ANY'
plotSeqContent(x, usePlotly = FALSE, labels, ...)

## S4 method for signature 'character'
plotSeqContent(x, usePlotly = FALSE, labels, ...)

## S4 method for signature 'FastqcData'
plotSeqContent(x, usePlotly = FALSE, labels, ...)

## S4 method for signature 'FastqcDataList'
plotSeqContent(
  x,
  usePlotly = FALSE,
  labels,
  pwfCols,
  plotType = c("heatmap", "line"),
  cluster = FALSE,
  dendrogram = FALSE,
  ...,
  nc = 2
)

Arguments

`x`	Can be a `FastqcData`, `FastqcDataList` or 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.
`...`	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
`plotType`	`character`. Type of plot to generate. Must be "line" or "heatmap"
`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`	Specify the number of columns if plotting a FastqcDataList as line plots. Passed to `ggplot2::facet_wrap`.

Details

Per base sequence content ( heatmap colours when plotting from multiple reports. The individual line plots are able to be generated by setting plotType = "line", and the layout is determined by facet_wrap from ggplot2.

Individual line plots are also generated when plotting from a single FastqcData object.

If setting usePlotly = TRUE for a large number of reports, the plot can be slow to render.

Value

A 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
plotSeqContent(fdl)

[Package ngsReports version 1.4.2 Index]