plotAssemblyStats {ngsReports}R Documentation

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)


[Package ngsReports version 1.2.0 Index]