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 1.10.0 Index]