plotHist: Plot the histogram of positive proportions
In UofABioinformaticsHub/rnaCleanR: Calculate strandness information of a bam file

Description Usage Arguments Value See Also Examples

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

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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, ...)

`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

If heatmap=FALSE: a ggplot object

getStrandFromBamFile, plotWin

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