plotWin: Plot the Proportion of + Stranded Reads

Description Usage Arguments Details Value See Also Examples

View source: R/plotWin.R

Description

Plot the number of reads vs the proportion of '+' stranded reads.

Usage

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plotWin(windows, split = c(10, 100, 1000), threshold = c(0.6, 0.7, 0.8,
0.9), save = FALSE, file = "win.pdf", group_by = NULL,
useCoverage = FALSE, ...)

Arguments

windows

data frame containing the strand information of the sliding windows. Windows should be obtained using the function getWinFromBamFile to ensure the correct data structure.

split

an integer vector that specifies how you want to partition the windows based on coverage. By default split = c(10,100,1000), partition windows into 4 groups based on these values.

threshold

a numeric vector between 0.5 & 1 that specifies which threshold lines to draw on the plot. The positive windows above the threshold line (or negative windows below the threshold line) will be kept when using filterDNA.

save

if TRUE, then the plot will be save into the file given by file parameter

file

the file name to save to plot

group_by

colnames of windows which will be used to split the plot

useCoverage

if TRUE then plot the coverage strand information, otherwise plot the number of reads strand information. FALSE by default

...

used to pass parameters to facet_wrap during plotting

Details

This function will plot the proportion of '+' stranded reads for each window, against the number of reads in each window. The threshold lines indicate the hypothetical boundary where windows will contain reads to kept or discarded using the filtering methods of filterDNA. Any plot can be easily modified using standard ggplot2 syntax (see Examples)

Value

The plot will be returned as a standard ggplot2 object

See Also

getWinFromBamFile, plotHist

Examples

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bamfilein = system.file('extdata','s2.sorted.bam',package = 'strandCheckR')
windows <- getWinFromBamFile(file = bamfilein,sequences = '10')
plotWin(windows)

# Change point colour using ggplot2
library(ggplot2)
plotWin(windows) + 
scale_colour_manual(values = rgb(seq(0, 1, length.out = 4), 0, 0))

strandCheckR documentation built on Nov. 1, 2018, 2:26 a.m.