plotInsertSize-methods: Plot Insert Size Distributions

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

Plot Insert Size Distributions

Description

Plot the insert size distribution from one of Fastp reports

Usage

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

## S4 method for signature 'FastpData'
plotInsertSize(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  plotType = c("histogram", "cumulative"),
  counts = FALSE,
  plotTheme = theme_get(),
  expand.x = 0.01,
  expand.y = c(0, 0.05),
  ...
)

## S4 method for signature 'FastpDataList'
plotInsertSize(
  x,
  usePlotly = FALSE,
  labels,
  pattern = ".(fast|fq|bam).*",
  plotType = c("heatmap", "line", "cumulative"),
  plotTheme = theme_get(),
  scaleFill = NULL,
  scaleColour = NULL,
  cluster = FALSE,
  dendrogram = FALSE,
  heat_w = 8,
  ...
)

Arguments

x	A FastpData or FastpDataList object
usePlotly	logical. Generate an interactive plot using plotly
labels	An optional named vector of labels for the file names. All file names must be present in the names of the vector.
pattern	Regex to remove from the end of any filenames
...	Passed to ⁠geom*⁠ functions during plotting
plotType	Determine the plot type. Options vary with the input structure
counts	logical(1) Plot read counts, or percentages (default)
plotTheme	a theme object
expand.x, expand.y	Axis expansions
scaleFill	Continuous scale used to fill heatmap cells. Defaults to the "inferno" palette
scaleColour	Discrete scale for adding line colours
cluster	logical default FALSE. If set to TRUE, data will be clustered using hierarchical clustering
dendrogram	logical redundant if cluster is FALSE if both cluster and dendrogram are specified as TRUE the dendrogram will be displayed.
heat_w	Width of the heatmap relative to other plot components

Details

Takes a Fastp os a set of Fastp reports and plot insert size distributions. Plots can be drawn as cumulative totals or the default histograms for a single report, and as boxplots or heatmaps for a set of reports

Value

A ggplot or plotly object

Examples

# Get the files included with the package
packageDir <- system.file("extdata", package = "ngsReports")
fl <- list.files(packageDir, pattern = "fastp.json.gz", full.names = TRUE)
fp <- FastpData(fl)
plotInsertSize(
  fp, counts = TRUE, fill = "steelblue4",
  plotTheme = theme(plot.title = element_text(hjust = 0.5))
)
plotInsertSize(fp, plotType = "cumulative")

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