curvePlot: Plot of Base Quality and GC Content.

In Rfastp: An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

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")

Rfastp documentation built on Nov. 8, 2020, 5:52 p.m.