plotHist: Plot the histogram of positive proportions

Description Usage Arguments Value See Also Examples

View source: R/plotHist.R

Description

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

Usage

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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

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

UofABioinformaticsHub/rnaCleanR documentation built on July 12, 2019, 10 p.m.