curvePlot {Rfastp} | R Documentation |
generate a ggplot2 object of Base Quality/GC content before and after QC.
curvePlot(json, curves = "quality_curves")
json |
the output json of function rfastq. [json] |
curves |
plots for Base Quality("quality_curves") or GC content("content_curves"). default is "quality_curves" |
a ggplot2 object.
Wei Wang
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")