plotAssemblyStats: Plot a summary of assembly logs

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

Plot a summary of assembly logs

Description

Plot a summary of assembly stats from a set of log files

Usage

plotAssemblyStats(
  x,
  type = c("quast", "busco"),
  usePlotly = FALSE,
  plotType = c("bar", "paracoord"),
  ...
)

Arguments

x	Paths to one or more log files
type	The tool used. Can be one of quast or busco
usePlotly	logical. If TRUE an interactive plot will be generated. If FALSE a ggplot object will be output
plotType	character. Plot type to output, one of bar or paracoord.
...	Used to pass additional attributes to theme() and between methods

Details

Loads a set of assembly log files and creates a default plot. Implemented tools are quast and BUSCO. quast will plot a parralel coordinate plot of some assembly statistics BUSCO will plot a stacked barplot of completeness statistics

Value

A ggplot2 object, or a plotly object

Examples

#getquast log filenames
quastFiles <- system.file("extdata",
c("quast1.tsv", "quast2.tsv"), package = "ngsReports")

# The default plot
plotAssemblyStats(quastFiles)

UofABioinformaticsHub/fastqcReports documentation built on April 1, 2024, 5:29 p.m.