plotHist: Plot the histogram of positive proportions

In UofABioinformaticsHub/strandCheckR: Calculate strandness information of a bam file

Description

Plot the histogram of positive proportions of the input data frame coming from getStrandFromBamFile

Usage

plotHist(windows, save = FALSE, file = "hist.pdf", groupBy = NULL,
  normalizeBy = 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 getStrandFromBamFile.
save	if TRUE, then the plot will be save into the file given by file parameter
file	the file name to save to plot
groupBy	the columns that will be used to split the data.
normalizeBy	instead of using the raw read count/coverage, we will normalize it to a proportion by dividing it to the total number of read count/coverage of windows that have the same value in the normalizeBy columns.
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

getStrandFromBamFile, plotWin

Examples

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

UofABioinformaticsHub/strandCheckR documentation built on Aug. 15, 2021, 9:08 a.m.