plotFastqcContent: Plot FastQC

In timflutre/rutilsfastqc: Utilitary functions to handle output from FastQC

Description

Plot a variable content (adapter or N) as percentage along the sequences per entry in a set of zip archives generated by FastQC. To be used after extractFastqcAdpContents() or extractFastqcBaseNs().

Usage

plotFastqcContent(content, max.datasets.per.plot = 25, lowest.perc = NULL,
  highest.perc = NULL, ylab = "Content (%)", main = "Quality control",
  legend.x = "topleft", legend.y = NULL, legend.cex = 1,
  add.2nd.yaxis = TRUE)

Arguments

content	return value from extractFastqcAdpContents() or extractFastqcBaseNs()
max.datasets.per.plot	max number of datasets on the same plot
lowest.perc	lowest percentage of content for the y-axis
highest.perc	highest percentage of content for the y-axis
ylab	a title for the y axis
main	an overall title for the plot
legend.x	x coordinate to position the legend (no legend if NULL)
legend.y	y coordinate to position the legend
legend.cex	numeric character expansion factor for legend labels
add.2nd.yaxis	add a 2nd y-axis on the right side of the plot

Value

nothing

Author(s)

Timothee Flutre [cre,aut], Nicolas Rode [ctb]

timflutre/rutilsfastqc documentation built on May 31, 2019, 2:16 p.m.