curvePlot {Rfastp} | R Documentation

## Plot of Base Quality and GC Content.

### Description

generate a ggplot2 object of Base Quality/GC content before and after QC.

### Usage

    curvePlot(json, curves = "quality_curves")

### Arguments

`json` | the output json of function rfastq. [json]
`curves` | plots for Base Quality("quality_curves") or GC content("content_curves"). default is "quality_curves"

### Value

a ggplot2 object.

### Author(s)

Wei Wang

### Examples

    outputPrefix <- tempfile(tmpdir = tempdir())
    se_read1 <- system.file("extdata","Fox3_Std_small.fq.gz",package="Rfastp")
    se_json_report <- rfastp(read1 = se_read1, outputFastq = outputPrefix,
       thread = 4)
    # Base Quality plot is the default output:
    p1 <- curvePlot(se_json_report)
    p1

    p2 <- curvePlot(se_json_report, curves = "content_curves")

[Package Rfastp version 1.2.0 Index]