plotHist: Plot the histogram of positive proportions

In strandCheckR: Calculate strandness information of a bam file

Description

Plot the histogram of positive proportions of the input histogram data frame

Usage

plotHist(windows, save = FALSE, file = "hist.pdf", group_by = NULL,
normalize_by = NULL, split = c(10, 100, 1000), breaks = 100,
useCoverage = FALSE, heatmap = FALSE, ...)

Arguments

windows	data frame containing the strand information of the sliding windows. Windows can be obtained using the function getWinFromBamFile.
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	the column names of windows that will be used to group the data
normalize_by	the column names of windows that will be used to normalize the read count or read coverage into proportion
split	an integer vector that specifies how you want to partition the windows based on the coverage. By default split = c(10,100,1000), which means that your windows will be partitionned into 4 groups, those have coverage < 10, from 10 to 100, from 100 to 1000, and > 1000
breaks	an integer giving the number of bins for the histogram
useCoverage	if TRUE then plot the coverage strand information, otherwise plot the number of reads strand information. FALSE by default
heatmap	if TRUE, then use heat map to plot the histogram, otherwise use barplot. FALSE by default.
...	used to pass parameters to facet_wrap

Value

If heatmap=FALSE: a ggplot object

See Also

getWinFromBamFile, plotWin

Examples

bamfilein = system.file('extdata','s1.sorted.bam',package = 'strandCheckR')
win  <- getWinFromBamFile(file = bamfilein,sequences='10')
plotHist(win)

strandCheckR documentation built on Nov. 8, 2020, 7:02 p.m.