plot.depth: Visualize sequencing depth and coverage at different levels

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

Visualizing sequencing depth and coverage at different levels.

Usage

plot.depth <- function(df, 
        left.jitter.amount=0.15, left.bp.notch=T, left.bp.ylim=c(0,300), left.bp.outline=F, left.bp.main="CCDS", left.bp.cex.main=0.8, left.bp.axis.label='CCDS',
        right.jitter.amount=0.3, right.bp.notch=T, right.bp.ylim=c(0.7,1), right.bp.outline=F, right.bp.main="Cov", right.bp.cex.main=0.8, right.bp.axis.labels=NA,
		left.bp.point.col=rgb(0.9, 0.5, 0.5, alpha=0.8),
		right.bp.point.col=rgb(0.9, 0.4, 0.5, alpha=0.8),
        pdffile=NA)

Arguments

df	A data frame containing sequencing depth coverage at different levels.
left.jitter.amount	Amount pass to jitter(amount=), controls noise level.
left.bp.notch	Pass to boxplot(notch=).
left.bp.ylim	Pass to boxplot(ylim=).
left.bp.outline	Pass to boxplot(outline=).
left.bp.main	The title.
left.bp.cex.main	Size of cex.main.
left.bp.axis.label	Axis label.
right.jitter.amount	Amount pass to jitter(amount=), controls noise level.
right.bp.notch	Pass to boxplot(notch=).
right.bp.ylim	Pass to boxplot(ylim=).
right.bp.outline	Pass to boxplot(outline=).
right.bp.main	The title.
right.bp.cex.main	Size of cex.main.
right.bp.axis.label	Axis label.
left.bp.point.col	color for the points.
right.bp.point.col	color for the points.
pdffile	If set, save figure to file.

Details

df has 8 columns, i.e.
sample, =0X, >=1X, >=4X, >=10X, >=20X, and average_depth
for example:
TB6111 0.017483 0.982517 0.948189 0.900967 0.839802 112.070764
27706A1 0.017566 0.982434 0.951066 0.908361 0.854066 125.642517
TB5539 0.012896 0.987104 0.960002 0.920660 0.871974 129.513491

See Also

plot.landscape, plot.MH

Examples

data("ccds.depth")
plot.depth(ccds.depth)

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.